RetrogeneDB ID: retro_ptro_2662

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:145110944..145111634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSPTRG00000016081
• Aliases: None
• Description: None

Sequence

>retro_ptro_2662
GTTGATGTAACCCCTAAAGAAATTGTTCTTGCTGATGTTATTGATAATGATTCCTGGAGACTCTGGCCATCAGTAGATGG
AAGCCAACAGAAAGACAAACAGCCTCATCAGGACCTCAAAGAAGTAACTTCTGAAGGGCTCAAGATGGTTAAAGAAAAAC
TTAGAGTGGGTTGCAGAGAGAGAAGAGTTGCTTTTGAAATTAGAAAGTCTGTGCGGGATGGCAGTATTGGTAGGCTCTAC
TTCTGATCTTGGCCACTGTGAAAAAATCAAGAAGGCCTGTGGAAATCTTGGCATTTCCTGAGAACTTCAAGTAACATCTG
TGCATAAAGGACCAGATAAAACTCTGAGGATTAAAGGTGAGTGTGAAGGGGATGGCATTCCCACTGTGTTTGTGGCAGTG
GCAGGCAGAAGAAATGGTTTGGGACCAGTGACGTCTGGGAACACTGCATATCCAGTTATCAGCTGTCCTCCGCTCAAGCA
GACTGGGGAGCTCAGGATGTGTGGTCTTCTCCTCGACTACCCAGTGGTCTCAGCTGCTCAACCACCCTTTCTCCAGAAGG
ATCAGCTCAGTTTGCTGCACAGATATTTGGGTTAAACAACCATTTGCTGTGGGGCAGACTGTGAGCAAGCGTTCTGAACA
CATGGATTTTCTTGAAGCAGGTTGACAAGGAAATCAGAGAACGTAATTTA

Alignment

ORF - retro_ptro_2662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 54.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDVTTKEIVLADVIDNDSWRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVK-KNFEWVAERVELLLKSES
          VDVT.KEIVLADVIDNDSWRLWPS.D.SQQKDKQ...DLKEVT.EGL.MVK.KN.EWVAER.ELLLK.ES
Retrocopy VDVTPKEIVLADVIDNDSWRLWPSVDGSQQKDKQPHQDLKEVTSEGLKMVK>KNLEWVAEREELLLKLES

Parental  QCRVVVLMGSTSDLGHCEKIKKACGSFGIPCELRVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNG
          .C...VL.GSTSDLGHCEKIKKACG..GI..EL.VTS.HKGPD.TLRIK.E.EGDGIPTVFVAVAGR.NG
Retrocopy LCGMAVLVGSTSDLGHCEKIKKACGNLGIS*ELQVTSVHKGPDKTLRIKGECEGDGIPTVFVAVAGRRNG

Parental  LGPVMSGNTAYPVISCPPL-TPDWGAQDVWSSLRLPSGLGCSTILSPEGSAQFAAQIFGLSNHLVWSKLR
          LGPV.SGNTAYPVISCPPL...DWGAQDVWSS.RLPSGL.CST.LSPEGSAQFAAQIFGL.NHL.W..L.
Retrocopy LGPVTSGNTAYPVISCPPL<QADWGAQDVWSSPRLPSGLSCSTTLSPEGSAQFAAQIFGLNNHLLWGRL*

Parental  ASILNTWISLKQADKKIRECNL
          AS.LNTWI.LKQ.DK.IRE.NL
Retrocopy ASVLNTWIFLKQVDKEIRERNL

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	29.65 RPM
SRP007412_cerebellum	0.00 RPM	43.59 RPM
SRP007412_heart	0.00 RPM	15.51 RPM
SRP007412_kidney	0.00 RPM	38.65 RPM
SRP007412_liver	0.00 RPM	69.36 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_2662 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2662 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3802
Homo sapiens	retro_hsap_3915

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662 , retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,