RCNE 33 and Fish SINE31

1
CR1-related
5S rRNA-related
SINE3-1
5
3
2
CTAATGCCCCAGTAAAGTG-AAGGGGACACTATACTGTCAGTGGGCGCCG
TCTTTCGGATGAGACGTTAAACCGAGGTCCTGACTCTCTGTGGTCATTAA
AAATCCCATGGCACTTCTCGTAAAGAGTAGGGGTG----TAACCCCGGTG
TCCTGGCCAAATTCC CTGATGCCCCAGCATGGTATGAAGGGGCACTGCA
CTGCTGG-AGGTGTCGTCTAATGGATGAGG-GTAAAACCAAGGTCTTGAC
CACCAGCAGTTATTAAAAATCCCATGGCACTTTTCA-AAAGAGTAAAGAT
GATGTTAAACCCTGTGTCCTGGCTAATTTCC CTGATGCCCCAGCATGGT
ATGAAGGGGCACTGCACTGCTGG-AGGTGTCGTCTAATGGATGAGG-GTA
AAACCAAGGTCTTGACCACCAGCAGTTATTAAAAATCCCATGGCACTTTT
CA-AAAGAGTAAAGATGATGTTAAACCCTGTGTCCTGGCTAATTTCC CT
GGTGCCCCGGCATGGTATGAGGGGGCACCGCACTGCTGG-AGGTGTCGTC
TAATGGATGAGG-GTAAAACCAAGGTCCTGACCACCAGCAGTTATTAAAA
ATCCCATGGCACTTTTCA-AAAGAGTAAAGATGATGTTAAACCCTGTGTC
CTGGCTAATTTCC CTGATGCCCCAGCATGGTATGAGGGGGCACCGCACT
GCTGG-AGGTGTCGTCTAATGGATGAGG-GTAAAACCAAGGTCCTGACCA
CCAGCAGTTATTAAAAATCCCATGGCACTTTTCA-AAAGAGTAAAGATGA
TGTTAAACCCTGTGTCCTGGCTAATTTCC CTGATGCCCCAGCATGGTAT
GAGGGGGCACCGCACTGTTGG-AGGTGTCGTCTAATGGATGAGG-GTAAA
ACCAAGGTCCTGACCACCAGCAGTTATTAAAAATCCCATGGCACTTTTCA
-AAAGAGTAAAGATGATGTTAAACCCTGTGTCCTGGCTAATTTCC CTGA
TGCCCCAGCATGGTATGAGGGGCCACCGCACTGTTGG-AGGTGTCGTCTA
ATGGATGAGG-GTAAAACCAAGGTCCTGACCACCAGCAGTTATTAAAAAT
CCCATGGCACTTTTCA-AAAGAGTAAAGATGATGTTAAACCCTGTGTCCT
GGCTAATTTCC CTGATGCCCCAGCATGGTATGAGGGGGCACAGCACTGC
TGG-AGGTGTCGTCTAATGGATGAGG-GTAAAACCAAGGTCCTGACCACC
AGCAGTTATTAAAAATCCCATGGCACTTTTCA-AAAGAGTAAAGATGATG
TTAAACCCTGTGTCCTGGCTAATTTCC CTGATGCCCCAGCATGGTATGA
GGGGGCACTGCACTGCTGG-AGGTGTCGTCTAATGGATGAGG-GTAAAAC
CAAGGTCTTGACCACCAGCAGTTATTAAAAATCCCATGGCACTTTTCA-A
AAGAGTAAAGATGATGTTAAACCCTGTGTCCTGGCTAATTTCC CTGATG
CCCCAGCATGGTATGAGGGGGCACTGCACTGCTGG-AGGTGTCGTCTAAT
GGATGAGG-GTAAAACCAAGGTCTTGACCACCAGCAGTTATTAAAAATCC
CATGGCACTTTTCA-AAAGAGTAAAGATGATGTTAAACCCTGTGTCCTGG
CTAATTTCC CTGATGCCCCAGCATGGTATGAGGGGGCACTGCACTGCTG
G-AGGTGTCGTCTAATGGATGAGG-GTAAAACCAAGGTCTTGACCACCAG
CAGTTATTAAAAATCCCATGGCACTTTTCA-AAAGAGTAAAGATGATGTT
AAACCCTGTGTCCTGGCTAATTTCC CTGATGCCCCAGCATGGAATGAGG
GGGCACTGCACTGCTGG-AGGTGTCGTCTAATGGATGAGG-GTAAAACCA
AGGTCCTGACCACCAGCAGTTATTAAAAATCCCATGGCACTTTTCA-AAA
GAGTAAAGATGATGTTAAACTCTGTGTCCTGGCTAATTTCC CTGATGCC
CCAGAATGGTACGAGGGGGCACTTCGCTGCTGG-AGGTGTCGTCTAATGG
ATGAGG-GTAAAACCAAGGTCCTGACCACCAGCAGTTATTAAAAATCCCA
TGGCACTTTTCA-AAAGAGTAAAGATGATGTTAAACCCTGTGTCCTGGCC
AATTTCC
SINE3-1 human Chimp Cavia Tenrec Mouse Rat
Elephant Dog Cow RheMac Armadillo Monodelphis
3
a) Alignment of paralogous human sequences and
SINE3-1.
Red A Green T Blue C Orange G

• Conservation profile of aligned human copies.

RED conserved between human/mouse/rat/dog.
BLUE not conserved
4
a) Alignment between coelacanth, SINE3-1 and
human consensus
Coelacanth CCCTNGCATGGCATCTGGGGGCAGGCTGTGCTGT
TGA-AGGGGCCGTCTTTCAGATGAGA SINE3-1
CCCCAGTAAAGTG-AAGGGGACA--CTATACTGTCAGTGGGCGCCGTCTT
TCGGATGAGA Human CCCCAGCATGGTATGAAGGGGCA
--CTGCACTGCTGG-AGGTGTCGTCTAATGGATGAGG

Coelacanth
CGATAAACNGAGGTCCTGTCTACTCTCTGTGGACATTAAAGATCCCATGG
CACCTTTTGC SINE3-1 CGTTAAACCGAGGTCCTGACTCT
---CTGTGGTCATTAAAAATCCCATGGCACTTCTCGT Human
GTA-AAACCAAGGTCTTGACCAC---CAGCAGTTATTAAAAATCCC
ATGGCACTTTTCA-

Coelacanth AAAGAGTAGGGGT---GTTAACCCCAGTGTCC
TGGCTATAAATCCC SINE3-1 AAAGAGTAGGGGTG----T
AACCCCGGTGTCCTGGCCA-AATTCCC Human
AAAGAGTAAAGATGATGTTAAACCCTGTGTCCTGGCTA--ATTTCC


5
GCCATATCACCCTGCA---GCCCAAGACCGGTTACTCACTGAAGCTAAGC
AGGGCTGAGCCTGGTCAGTACCTGGATGGGAGACCACATGGGAAAACTAG
GTTGCTGTTGG

GCCATACCACCCTGAACGCGCCCGAT
CTCGTCTGATCTCGGAAGCTAAGCAGGGTCGGGCCTGGTTAGTACTTGGA
TGGGAGACCGCCTGGGAATACCGGG-TGCTGTAGG
5S rRNA
SINE3-1
5S rRNA
SINE3-1
Human
Coelacanth
tRNA-Val
TGGTGGCTCAGTAGGTAGCACTCTTGCCTCTGAGTCAGAGGGTCATGGGT
TCAAAT
TGGTGGCTCAGTGGTTAGCACTTTTACCTCACA
GGAAGAAGGTCGCTGGTTCAAGT
Coelacanth
tRNA-Val
6
a) Alignment of paralogous coelacanth sequences
and SINE3-1.
SINE3-1
Coelacanth copies
7
a) The internal region is shared by a SINE
element in the sea urchin genome.
coelacanth GCATGGCATCTGGGGGCAGGCTGTGCT--GTTGA
AGG-G-GCCGTCTTTCAGATGAGACG SINE3-1
GTAAAGTG---AAGGGGACACTATACT--GTCAGTGG-GCGCCGTCTTTC
GGATGAGACG SINE2-3_SP CCCTTGTTCATAGACGCAGGTTA
TGTCAAGTGGAAAACACTCCGTCCCTCGGATAGGACG

coelacanth
ATAAACNGAGGTCCTGTCT-----------ACTCTCTGTGGACATTAAAG
ATCCCATGGC SINE3-1 TTAAACCGAGGTCCTG-------
-------ACTCTCTGTGGTCATTAAAAATCCCATGGC SINE2-3_SP
TTAAATGGAGGCCCCGTGTAGAGAAGAGTCACTACCTTTGCACGTT
AAGAA-CCCACTGC

coelacanth ACCTTTTGCA-AAGAGTAGGGGTGTTAACC
CCAGTGTCCTGG-CTATAAAT---CCCCCA SINE3-1
ACTTCTCGTA-AAGAGTAGGGGTGT-AACCCCGGTGTCCTGG-CCAAATT
C---CCTCCA SINE2-3_SP ACTATTCGTATAAGAGTAGGGGG
A--AACCCCGGTGTAGTGGTCCACCTGCACACCCCAA


8
a) The internal region is shared by a SINE
element in the sea urchin genome.
Coelacanth AACNGAGGTCCTGTCTACTCTCTGTGGACATTA
AAGATCCCATGGCACCTTTTGCAAAGA Schistosoma
-------------------------GGTCATTAAAGATCCCATGGCACTA
ATCGTAA-GA SINE31 AACCGAGGTCCTG---ACTCTC
TGTGGTCATTAAAAATCCCATGGCACTTCTCGTAAAGA RCNE33
AACCAAGGTCTTG---ACCACCAGCAGTTATTAAAAATCCCATG
GCACTTTTCA-AAAGA

Coelacanth GTAGGGGTG---TTAACCCCAGTGTCCTG
GCTATAAATCCCCCAGAGNGCTTTGAGATCC Schistosoma
GTAGCTGTG---TTAACCCCGGTGTCCTGGCTA--AATTCCC--------
---------- SINE31 GTAGGGGTG----TAACCCCGG
TGTCCTGGCCAAATTCCCTCCATCGGCCCTTACGCATC RCNE33
GTAAAGATGATGTTAAACCCTGTGTCCTGGCTAATTTCC-----
----------------