RetrogeneDB ID: retro_ggor_2749

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:98449741..98450565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSGGOG00000006582
• Aliases: None
• Description: None

Sequence

>retro_ggor_2749
CCAGCAGAAAAGAATGCTGACCTTTGTAAGGAGATAGTGGATGGGTTAAGAATAACCTTTGATTACACTACCGCATCAGT
TATAATCTATCCATGGGAATAAGCTCAGTATAAAAAGGTGACTTCAGCTAAGTGTTTTCTTTCAATTACGGAAAGCACCA
CAGACAATAAAATGAGCCAGGGGGAGCTCTCTCCCAGCCCACCTTTGTTGAATCCATCCACACCACGGTCCACAGAGAGT
CAGACAACCACAGCTGAACCAGCCACCCACAAAAGGCACAAAGCCAAGCCGGAAGCATTGCAGGCTCTGAGGCGGTCTGC
GTGCCACACCACCAACTGCAACAGGCTGGCTGAGAGCAGGCGTCACCTCGCCCAAGTGCCAGCAGCAGGCCACATCTACT
AGCACGCCCCAGGCTGCTCCTGAACCTGGAGAACAAAACACCTGTGCATCATCTTCAACTATTCCTCAGCCTCCTAGCAA
GGAAGAAAGTGCTGCATTTACTGGCTTTGAAGGGAAAAGAACTAATTAAATAAATGAGGTCCTCTCGTGGAAGCTTGTGC
CTGATAATTACCACCCAGGTGACCAGACACCTCCACCCCCTTCACATTTATGGGGCACAACATTTGCTGTGACTTTCAGT
AAAACTTCCAGAAATCCTTGGAAACATGTCCTAGTCTGAGAAGAATCTGAAGGCTTTACTGAAACACTTTGATCTTTTCT
GAAGTTTTTAGCAGAATATATACCATGATGATTTCTTCCCAGAGTTGGCTTATGTTGCTGCCTATGAGGCATATTATAGC
ACCTAGAAACCCCCGGCAATTTAT

Alignment

ORF - retro_ggor_2749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.96 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLL
          PAEKN.DLCKE.VDGLRITFDYT...V..YP.E.AQYKKVTS.K.FL.I.ES.T....SQ.ELSPSPPLL
Retrocopy PAEKNADLCKEIVDGLRITFDYTTASVIIYPWE*AQYKKVTSAKCFLSITESTTDNKMSQGELSPSPPLL

Parental  NPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSES-SASPQPKRRQQDTSASMPKL
          NPSTP.STESQ.TT.EPAT.KR.KA.PEALQ.LRRS..H..NC.RL.ES..ASP.P...........P.L
Retrocopy NPSTPRSTESQTTTAEPATHKRHKAKPEALQALRRSACHTTNCNRLAES<QASPRPSASSRPHLLARPRL

Parental  FLHLEKKETPVH-SRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPS-YIY
          .L.LE.K.TPVH.S.S..P.P..PSKE.SA.F.GFEG.RTN.INEVLSWKLVPDNY.PGDQ.PPP...IY
Retrocopy LLNLENK-TPVH<SSSTIPQP--PSKEESAAFTGFEGKRTN*INEVLSWKLVPDNYHPGDQTPPPP>HIY

Parental  GAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDL-FLRFLAEY-HDDFF-PESAYVAACEAHYSTKNPR
          GAQHLL.L.VKLPEILG.MS.SEKNLKALLKHFDL.FL.FLAEY...D.F.PE.AYVAA.EA.YST..P.
Retrocopy GAQHLL*LSVKLPEILGNMS*SEKNLKALLKHFDL<FLKFLAEY>YHDDFFPELAYVAAYEAYYST*KPP

Parental  AIY
          AIY
Retrocopy AIY

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	24.36 RPM
SRP007412_cerebellum	0.08 RPM	13.47 RPM
SRP007412_heart	0.00 RPM	3.63 RPM
SRP007412_kidney	0.00 RPM	13.37 RPM
SRP007412_liver	0.00 RPM	14.16 RPM
SRP007412_testis	0.00 RPM	32.94 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2749 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4097
Pan troglodytes	retro_ptro_2778
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,