RetrogeneDB ID: retro_ptro_2773

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:85734074..85734715(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSPTRG00000018662
• Aliases: None
• Description: None

Sequence

>retro_ptro_2773
AAGTTGGGTGATCATGAAGCTATTAGGCAAGCAATTCTTGGTCCTGCCCATTTGGAGAACTATGCTTAGAAAATGTTTTT
ATACTCAGACAATGATCATGCTGGGTGATTTCACAAGATGATCAAGCCCTTTTTATACTCCACAGTTTTAAATAGATGTC
ATAATAATATTATGACAACTCATTGATGAAAATGTGAAACACAGAAAGTATGTAAGATGAAAAGCAAAATATATTCATAT
TTGTTTAAAGAATGGGGAGCTGCCTCAACTAGTATCTGCTGGAATTGAAGAAGATAACAATATAACAATATTGCAGAAAA
TGAAAATGCTGAAGCAACCTATCTGTCCACTGAGCCATGTCAGCCACCATCTTCAACTTACGACCCAAGCCACATGCCAT
AAAGGAGCTATAACAGAATACAGATTCCTCCCAGTGCACACACTCCAGCTAATACATCAGTAGAAGTGCATCACAATGCA
GATGTAACAAATCTAATATCTACTCCAAAGACAATTCAGCAATTGAGCCCACATTTTTAGTAGTTTCTCAAAGCGATATC
CATCTAACACTAGAGGACTTTGTTAGTGATCAGAAATACAGCAAATAATAGGCTGGCAGTGCCTTGTCATATGAAGATAT
C

Alignment

ORF - retro_ptro_2773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.21 %
• Parental protein coverage: 70.36 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSF-YTASLLIDVITVFGELTDENVKH
          .LGD.EAI.Q.I.G.AHLENYA.KMFLY.DN.D.AG.FHK.MIK.F.YT....IDVI.....L.DENVKH
Retrocopy KLGDHEAIRQAILGPAHLENYA*KMFLYSDN-DHAG*FHK-MIKPF>YTPQF*IDVIIIL*QLIDENVKH

Parental  RKYARWKATYIHNCLKNGETPQAGPVGIEEDNDIEENEDAGAASLPTQP-TQPSS--SSTYDPSNMPSGN
          RKY.R.KA.YIH.CLKNGE.PQ....GIEEDN.I...........P..P.T.P....SSTYDPS.MP...
Retrocopy RKYVR*KAKYIHICLKNGELPQLVSAGIEEDNNITILQKMKMLKQPICP<TEPCQPPSSTYDPSHMP*RS

Parental  YTGIQIPPGAHAPANTPAEVPHSTGVASNTIQPTPQTI-PAIDPALFNTISQGDVRLTPEDFARAQKYCK
          Y..IQIPP.AH.PANT..EV.H...V.......TP.TI..AI.P..F...SQ.D..LT.EDF...QKY.K
Retrocopy YNRIQIPPSAHTPANTSVEVHHNADVTN--LISTPKTI<SAIEPT-FLVVSQSDIHLTLEDFVSDQKYSK

Parental  -YAGSALQYEDV
          ..AGSAL.YED.
Retrocopy **AGSALSYEDI

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	27.87 RPM
SRP007412_cerebellum	0.00 RPM	29.47 RPM
SRP007412_heart	0.00 RPM	16.82 RPM
SRP007412_kidney	0.00 RPM	22.10 RPM
SRP007412_liver	0.00 RPM	10.44 RPM
SRP007412_testis	0.00 RPM	13.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2773 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2773 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2773 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773 ,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,