RetrogeneDB ID: retro_btau_883

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:97070146..97071666(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000002180
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSBTAG00000009278
• Aliases: MSL3, MSL3L1
• Description: male-specific lethal 3 homolog [Source:RefSeq peptide;Acc:NP_001179333]

Sequence

>retro_btau_883
TCAGGAAAGAAAGCGCCGTGCTTCGAGCTTGACCCCACCAAGGCGCGAGTGCTCTACGATGCCAAAAATCGTCGATGTTT
TTGTTGGGAAAGACGAAAAAGGCAGAAAGATCCCAGAATATCTGATCCATTTTAATGGTTGGAACAGAAGTTGGGATAGA
TGAGCAGCAGAGGATCATGTCCGTGACGCCGATGAAAATCGGAGATTACGGCGGAAATTGGCCAAAAAGGCTGTAGCTCG
CCTGAGAAGCACAGGAAGAAAGAGGAAGCACGACAGGTTACCTGGGGTGGACTCTGTCTTAAAAGCCTCCCTGCTGACGA
GAAAGATGAAAACGAAGAAAACTCAATAAACAGTTCCTCTGACAGTGAAGAAAAGAACGGAGAAATAAGTGAAAAAAAAG
ATACTGAAAGTCTGAAGTGAAGGAAGGACCAGGGCTGCACGCAGAAAAAAAGGAAATGGAAGAAAGAACAGTAACTATAG
AAATCCCTGAAATTCTGAAGAAGAAGCTTGAGGATGATTGTTACTATATCAACAGGAGGAAACGGTTAGTGAAAGTTCCG
TGCCAGACCAACATCATAACTATTTTGGAATCATACATGAAGCATTTTGCTATCAATGCAGCCTTTTCAGCCAATGAGAG
GCCTCGTCACTATCATGCTATGCCACATGCCAACATGAATGTGCATTATATCCCAGCAGAAAAGAACGTTGACCTTTGTA
AGGAGATGGTGGATGGATTAAGAATAACCTTTGATTACACTCTCCCATTGGTTTTGCTCTATCCATACGAACGTGTTCAA
TATAAAAAGGTGACTTCGTCCAAATTGTTTCTTCCCATTAAGGAAAGTACCACAAACAATAATAGGAACCAGGAGGAGCT
CTCTCCAAGTCCACCTTTGTTGAATCCATCCACACCACAGTCCACAGAGAGTCAGCCAAACTCAGGTGAACCAACCACCC
CCAAAAGGCGCAAAGCCGAGCCGGAAGCCTTACAGTCCCTGAGGCGGTCCACGCGCCACTCTGCCAATTGCGACAGGCTG
TCCGAGAGCAGCGCCTCGCCTCAGCCCAAGCACCGGCAGCAGCACATGTCCGCCAGCATGCCCAAGCTATTCCTGTACCT
GGAAGAGAAGACATCTGTTCATAGCAGATCATCCTCGCCTGTTCCTCTGACCCCTAGCAAGGAAGGGAGTGCAGTGTTTG
CTGGCTTTGAAGGCAGAAGAACCAAAGAAATAAATGAGGTCCTCTCCTGGAAACTTGTACCTGATAGTTATCCTCCAGGT
GACCAACCACCTCCACCCTCTTACATTTATGGGGCGCAACACTTGCTGCGTTTGTTTGTGAAACTTCCTGAAATCCTTGG
AAAGATATCCTTTTCTGAGAAGAACCTGAAGGCTTTACTGAAGCACCTTGATCTCTTTCTGAGGTTTTTAGCAGAGTACC
ATGATGACTTCTTCCCAGAGTCTGCCTGTGTTGCTGCCTGTGAAGTGCACTACAGCAGGAAGAACCCCAGGGCGATTTAT

Alignment

ORF - retro_btau_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.06 %
• Parental protein coverage: 97.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGEKVLCFEPDPTKARVLYDAK-IVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRR
          SG.K..CFE.DPTKARVLYDAK.IVDV.VGKDEKGRKIPEYLIHFNGWNRSWDR.AAEDHV.RD.DENRR
Retrocopy SGKKAPCFELDPTKARVLYDAK>IVDVFVGKDEKGRKIPEYLIHFNGWNRSWDR*AAEDHV-RDADENRR

Parental  LQRKLAKKAVARLRSTGRKRKRCRLPGVDSV-LKSLPADEKDENDENSISSSSDSEEKDGEISEEGDTEE
          L.RKLAKKAVARLRSTGRKRK..RLPGVDSV.LKSLPADEKDEN.ENSI.SSSDSEEK.GEIS...DTE.
Retrocopy LRRKLAKKAVARLRSTGRKRKHDRLPGVDSV<LKSLPADEKDENEENSINSSSDSEEKNGEISXXXDTES

Parental  KTEVKEGPELHTKKE-MEERTITIEIPDVLKKKLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAIN
          ....K.......K...MEERT.TIEIP..LKKKLEDDCYYINRRKRLVK.PCQTNIITILESY.KHFAIN
Retrocopy LK*RKDQGCTQKKRK<MEERTVTIEIPEILKKKLEDDCYYINRRKRLVKVPCQTNIITILESYMKHFAIN

Parental  AAFSANERPRHHHVIPHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQVQYKKVTSSKF
          AAFSANERPRH.H..PHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYE.VQYKKVTSSK.
Retrocopy AAFSANERPRHYHAMPHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYERVQYKKVTSSKL

Parental  FLPIKESTTSTNRNQEELSPSPPLLNPSTPQSTESQPTSGEPTTPKRRKGEPEAFQSLRRSTRHSANCDR
          FLPIKESTT..NRNQEELSPSPPLLNPSTPQSTESQP.SGEPTTPKRRK.EPEA.QSLRRSTRHSANCDR
Retrocopy FLPIKESTTNNNRNQEELSPSPPLLNPSTPQSTESQPNSGEPTTPKRRKAEPEALQSLRRSTRHSANCDR

Parental  LSESSASPQPKRRQQDTSASMPKLFLHLEKKTPVHSRSSSPVPLTPSKEGSAVFAGFEGRRTNEINEVLS
          LSESSASPQPK.RQQ..SASMPKLFL.LE.KT.VHSRSSSPVPLTPSKEGSAVFAGFEGRRT.EINEVLS
Retrocopy LSESSASPQPKHRQQHMSASMPKLFLYLEEKTSVHSRSSSPVPLTPSKEGSAVFAGFEGRRTKEINEVLS

Parental  WKLVPDSYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFP
          WKLVPDSYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGK.SFSEKNLKALLKH.DLFLRFLAEYHDDFFP
Retrocopy WKLVPDSYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKISFSEKNLKALLKHLDLFLRFLAEYHDDFFP

Parental  ESAYVAACEAHYSTKNPRAIY
          ESA.VAACE.HYS.KNPRAIY
Retrocopy ESACVAACEVHYSRKNPRAIY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	35.98 RPM
ERP005899_muscle	0.00 RPM	37.01 RPM
SRP017611_brain	0.09 RPM	29.46 RPM
SRP017611_kidney	0.06 RPM	49.08 RPM
SRP017611_liver	0.15 RPM	26.35 RPM
SRP030211_testis	8.71 RPM	25.12 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_883 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883 ,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,