RetrogeneDB ID: retro_pabe_3353

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:105806737..105807848(-)
• Located in intron of: ENSPPYG00000018782

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSPPYG00000020123
• Aliases: MSL3, MSL3L1
• Description: Male-specific lethal 3 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R6Y9]

Sequence

>retro_pabe_3353
CAGATTGCTGTTGTTATTGGTGGGAATGACAAAAAAGGCAGAAAGATCCCAGAATATCTAATACATTTTAATAGTTGGAA
TGGAAGCTGTGATAGATGGGCAGCCAAAGATCATGTGCACTGTAATACAGGTGCAAATCAAGGATGACAGCATGAATTGG
CAAGAAAAGCTGCAGCTCACCTGAGAAGCACAGGAAGAAGGAAGTGCTGCAGGCTGTCTGGCATCAAATCTGTCTAAAAA
AGCCCCCCAGTTGAAGACAAAGATGAAAATGCTGAAAATTCAATAAGCAGTTCTCCAACAGTAGTGAAGACAAGGATGAA
AAATAAGTGAAGGAAGTGTTATTGAAGAAGAGACTTAAGTGCAAGAACTGGAGCTGTAAACAGAAAGGGAAATGGAAGAA
AGAATAATAACTATAGAAATCCCCAAAGTTCTGAACAAGTGGCTTGAGGGTGATCATTACTACATTAACAGAAGGAAACA
GTTAATGAGACTTCCACGACAGACCAACATCATAATGATTTTGGAGCCCCACGAGAAGCATTTTGCTATCAACACAGCTT
TTTCAGCCAGTGAGAGGCCTTGCCACCATCACACTATGTGGCAGCCAACATGAAGGTGCATTATATCCCAGCAGAAAAGA
ATGCTGACCTTTTTAAGGAGACGGTGGACGGGTTAAGAATAACCTTTGATTACACTACCCCATCAGTTATAATCTATCCA
TGGGAATAAGCTCAGTATAAAAAGGTGACTTCATCTAAGTGTTTTCTTTCAATTACAGAAAGCACCACAGACAACAAAAG
GAGCCAGGGGGAGCTCTCTCCCAGCTCACCTTTGTTGAATCCATCCACACCACGGTCCACAGACAGTCAGACAACCACAG
CTGAACCAGCCACCCACAAAAGGCACAAAGCCAAGCCGGAAGCATTGCAGGCTCTGAGGCGGTCCGCGTACCACACCACC
AACTGCAACAGGCTGGCTGAGAGCAGGCGTCACCTCGCGGAAGTGCCAGCAGCAGGACACATCGACTAGCATGCCCCAGG
CTGCTCCTGAACCTGGAGAAGAAAACACCTGTGCATCATCTTCAACTATTCCTCAGCCTCCTAGTAAGGAA

Alignment

ORF - retro_pabe_3353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.89 %
• Parental protein coverage: 72.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVARLRSTGRKKKR
          .I..VI.G.D.KGRKIPEYLIHFN.WN.S.DRWAA.DHV...T..N...Q..LARKA.A.LRSTGR.K..
Retrocopy QIAVVIGGNDKKGRKIPEYLIHFNSWNGSCDRWAAKDHVHCNTGANQG*QHELARKAAAHLRSTGRRKC-

Parental  CRLPGVDSVLKGLPTEEKDENDENSLSSS-SDCSENKDEE-ISEESDIEEKTEVKEEPELQTRREMEERT
          CRL.G..SV.K..P.E.KDEN.ENS.SSS.S..SE.KDE..ISE.S.IEE.T.V..E.EL.T.REMEER.
Retrocopy CRLSGIKSV*KSPPVEDKDENAENSISSS<SNSSEDKDEK<ISEGSVIEEET*V-QELEL*TEREMEERI

Parental  ITIEIPEVLKKQLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANERPRHHHVMPH-ANM
          ITIEIP.VL.K.LE.D.YYINRRK.L..LP.QTNII.ILE...KHFAIN.AFSA.ERP.HHH.M...ANM
Retrocopy ITIEIPKVLNKWLEGDHYYINRRKQLMRLPRQTNIIMILEPHEKHFAINTAFSASERPCHHHTMWQ<ANM

Parental  NVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSP
          .VHYIPAEKN.DL.KE.VDGLRITFDYT.P.V..YP.E.AQYKKVTSSK.FL.I.ES.T...RSQ.ELSP
Retrocopy KVHYIPAEKNADLFKETVDGLRITFDYTTPSVIIYPWE*AQYKKVTSSKCFLSITESTTDNKRSQGELSP

Parental  SPPLLNPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSES-SASPQ-PKRRQQDTS
          S.PLLNPSTP.ST.SQ.TT.EPAT.KR.KA.PEALQ.LRRS..H..NC.RL.ES..ASP...K..QQDTS
Retrocopy SSPLLNPSTPRSTDSQTTTAEPATHKRHKAKPEALQALRRSAYHTTNCNRLAES<QASPR<RKCQQQDTS

Parental  GSM-PKLFLHLEKKTPVH-SRSSSPIPLTPSKE
          .SM.P.L.L.LEKKTPVH.S.S..P.P..PSKE
Retrocopy TSM>PRLLLNLEKKTPVH<SSSTIPQP--PSKE

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	29.86 RPM
SRP007412_cerebellum	0.00 RPM	14.96 RPM
SRP007412_heart	0.09 RPM	5.36 RPM
SRP007412_kidney	0.07 RPM	10.24 RPM
SRP007412_liver	0.06 RPM	8.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3353 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3353 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,