RetrogeneDB ID: retro_ptro_2778

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:97611469..97612293(-)
• Located in intron of: ENSPTRG00000020464

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSPTRG00000021662
• Aliases: MSL3, MSL3L1
• Description: male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]

Sequence

>retro_ptro_2778
CCAGCAGAAAAGAATGCTGACCTTTGTAAGGAGATGGTGGATGGGTTAAGAATAACCTTTGATTACACTACCGCATCAGT
TATAATCTATCCATGGGAATAAGCTCAGTATAAAAAGGTGACTTCAGCTAAGTGTTTTCTTTCAATTACGGAAAGCACCA
CAGACAATAAAATGAGCCAGGGGGAGCTCTCTCCCAGCCCACCTTTGTTGAATCCATCCACACCACGGTCCACAGAGAGT
CAGACAACCACAGCTGAACCAGCCACCCACAAAAGGCACAAAGCCAAGCCGGAAGCAGTGCAGGCTCTGAGGCGGTCCGC
GTGCCACACCACCAACTGCAACAGGCTGGCTGAGAGCAGGCGTCACTTCGTCCAAGTGCCGGCAGCAGGCCACATCTACT
AGCACGCCCCAGGCTGCTCCTGAACCTGGAGAACAAAACACCTGTGCATCATCTTCAACTATTCCTCAGCCTCTTAGCAA
GGAAGAAAGTGCTGCATTTACTGGCTTTGAAGGGAAAAGAACTAATTAAATAAATGAGGTCCTCTCGTGGAAGCTTGTGC
CTGATAATTACCACCCAGGTGACCAGACACCTCCACCCCCTTCACATTTATGGGGCACAACATTTGCTGTGACTTTTGGT
AAAACTTCCAGAAATCCTTGGAAACATGTCCTAGTCTGAGAAGAATCTGAAGGCTTTATTGAAACACTTTGATCTTTTCT
GAAGTTTTTAGCAGAATATATACCATGATGATTTCTTCCCAGAGTTGGCTTATGTTGCTGCCTATGAGGCATATTATAGC
ACCTAGAAACCCCCGGCAATTTAT

Alignment

ORF - retro_ptro_2778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.83 %
• Parental protein coverage: 53.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLL
          PAEKN.DLCKEMVDGLRITFDYT...V..YP.E.AQYKKVTS.K.FL.I.ES.T....SQ.ELSPSPPLL
Retrocopy PAEKNADLCKEMVDGLRITFDYTTASVIIYPWE*AQYKKVTSAKCFLSITESTTDNKMSQGELSPSPPLL

Parental  NPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSES-SASPQP-KRRQQDTSAS-MP
          NPSTP.STESQ.TT.EPAT.KR.KA.PEA.Q.LRRS..H..NC.RL.ES..AS..P.K.RQQ.TS.S..P
Retrocopy NPSTPRSTESQTTTAEPATHKRHKAKPEAVQALRRSACHTTNCNRLAES<QASLRP<KCRQQATSTS>RP

Parental  KLFLHLEKKTPVH-SRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPS-YI
          .L.L.LE.KTPVH.S.S..P.PL..SKE.SA.F.GFEG.RTN.INEVLSWKLVPDNY.PGDQ.PPP...I
Retrocopy RLLLNLENKTPVH<SSSTIPQPL--SKEESAAFTGFEGKRTN*INEVLSWKLVPDNYHPGDQTPPPP>HI

Parental  YGAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDL-FLRFLAEY-HDDFF-PESAYVAACEAHYSTKNP
          YGAQHLL.L.VKLPEILG.MS.SEKNLKALLKHFDL.FL.FLAEY...D.F.PE.AYVAA.EA.YST..P
Retrocopy YGAQHLL*LLVKLPEILGNMS*SEKNLKALLKHFDL<FLKFLAEY>YHDDFFPELAYVAAYEAYYST*KP

Parental  RAIY
          .AIY
Retrocopy PAIY

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	0.05 RPM	18.12 RPM
SRP007412_cerebellum	0.00 RPM	21.11 RPM
SRP007412_heart	0.00 RPM	8.07 RPM
SRP007412_kidney	0.00 RPM	14.15 RPM
SRP007412_liver	0.00 RPM	11.92 RPM
SRP007412_testis	0.00 RPM	34.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2778 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2778 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4097
Gorilla gorilla	retro_ggor_2749
Callithrix jacchus	retro_cjac_1490

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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,