RetrogeneDB ID: retro_ptro_2617

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:39387316..39388590(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSPTRG00000018760
• Aliases: None
• Description: Pan troglodytes t-complex 1 (TCP1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246572]

Sequence

>retro_ptro_2617
ATGGAGAGGCCTTTGTCCGTGTTTGGGGACTGCAGCACTGGGGAGGCGATCTGCTCCCAGAACGTTATGGCTGCAGCTTT
GATTGCCAATACTGTAAAAAGTTCTCTTGGTCCAGTTGGCTTGGTTAAAATGTTGGTGGATGATACTGGTGATGTATCCA
TTACTAACGGTGGTGCACCATCCTGAAGTTACTGGAGGTAGAACATCCTGCAGCTAAAGTTCTTTGTGAGCTGGCTGATC
TGCAAGACAAAGAAGTTGGAGATGGAACTACCTCCGTGGTTATTATTGCAGCAGAACTCCTAAAAAATGAAGATGAATTA
GTCAAACAGAAAATTCATCCCACGTCAGTTATTAGTGGCTATGGACTTGCTTGCAAGGAAGCAGTGCGTTATATCAATGA
AAACCTAATTGTTAACACAGATAAAGTGGGAAGAGATTGCCTGATTAATGCTGCCAAGACATCCACGTCTTCCAAAATCA
TTGGAATAAATGGTGATTTCTTTGCTAACATGGTAGTAGATGCTGTATTTGCTATTAAATACACAGACATAAGAGGCCAG
CCATGCTATCCAGTCAATTCTGCTAATATTTTGAAAGCCCATGGGAAAAGTCAAACAGAGAGTATGCTCATCAGTGGCTA
TGCATTCAACTGTGTGGTGGGATCCCAGGGCATACCCAAGAGAATTGTAAATGCAAAAATTGCTTGCCTTGACTTTGGCC
TGCAAAAAACAAAAATGAAGCTTGGTATACAGGTGGTCATTACAGACCCTGAAAAACTGGACCAAATTAGACAGAGAGAA
TCAGATATTACCAAGGAGAGAATTCAGAAGATCCTGGTAACTGGTGCCAGCATTATTCTAACCACTGGTGGAATTGATGA
TATGTGTCTGAAGTATTTTGTGGAGGCTGGTGCTACGGCAGTTAGAAGAGTTTTTAAAAGGGACCTTAAACGCATTCCGA
AAGCTTCTGGAGCAACTATTCTGTCAACTCTGGCCAATTTGGAAGATAAAGAAACTTTTGAAGCTGTAGTGTTGGGGTAG
GCAGAAGAAGTGGTATAGCAGAGAATTTGTGATGATGAGCTGATCTTAATCAAAAACACTAACCCTCATACATTTGCATC
GATTATCTTACGTGGGACAAATGATTACATGTGTGATGAGATGAAGCATTCTTTACATGATGCTTTTTGTGTAGTGAAGA
TAGTTTTGGTGTCAAAATCTGTGGTTCCAGGTGTGGGTGCTGCAGAAGTAGCCCTTTCTATATACCTTGAAAAC

Alignment

ORF - retro_ptro_2617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.79 %
• Parental protein coverage: 76.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGPLSVFGDRSTGETIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGA-TILKLLEVEH
          ME.PLSVFGD.STGE.I.SQNVMAAA.IAN.VKSSLGPVGL.KMLVDD.GDV.ITN.GA.TILKLLEVEH
Retrocopy MERPLSVFGDCSTGEAICSQNVMAAALIANTVKSSLGPVGLVKMLVDDTGDVSITNGGA<TILKLLEVEH

Parental  PAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIVN
          PAAKVLCELADLQDKEVGDGTTSVVIIAAELLKN.DELVKQKIHPTSVISGY.LACKEAVRYINENLIVN
Retrocopy PAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNEDELVKQKIHPTSVISGYGLACKEAVRYINENLIVN

Parental  TDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDIRGQPRYPVNSVNILKAHGRSQMESM
          TD..GRDCLINAAKTS.SSKIIGINGDFFANMVVDAV.AIKYTDIRGQP.YPVNS.NILKAHG.SQ.ESM
Retrocopy TDKVGRDCLINAAKTSTSSKIIGINGDFFANMVVDAVFAIKYTDIRGQPCYPVNSANILKAHGKSQTESM

Parental  LISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKIL
          LISGYA.NCVVGSQG.PKRIVNAKIACLDF.LQKTKMKLG.QVVITDPEKLDQIRQRESDITKERIQKIL
Retrocopy LISGYAFNCVVGSQGIPKRIVNAKIACLDFGLQKTKMKLGIQVVITDPEKLDQIRQRESDITKERIQKIL

Parental  ATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQAE
          .TGA..ILTTGGIDDMCLKYFVEAGA.AVRRV.KRDLKRI.KASGATILSTLANLE..ETFEA..LG.AE
Retrocopy VTGASIILTTGGIDDMCLKYFVEAGATAVRRVFKRDLKRIPKASGATILSTLANLEDKETFEAVVLG*AE

Parental  EVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEAAL
          EVV..RICDDELILIKNT...T.ASIILRG.ND.MCDEM..SLHDA.CVVK.VL.SKSVVPG.GA.E.AL
Retrocopy EVV*QRICDDELILIKNTNPHTFASIILRGTNDYMCDEMKHSLHDAFCVVKIVLVSKSVVPGVGAAEVAL

Parental  SIYLEN
          SIYLEN
Retrocopy SIYLEN

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	0.04 RPM	67.48 RPM
SRP007412_cerebellum	0.00 RPM	96.47 RPM
SRP007412_heart	0.06 RPM	67.88 RPM
SRP007412_kidney	0.08 RPM	88.99 RPM
SRP007412_liver	0.00 RPM	88.74 RPM
SRP007412_testis	0.11 RPM	295.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2617 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2617 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3722
Gorilla gorilla	retro_ggor_2514
Macaca mulatta	retro_mmul_1696

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617 ,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,