RetrogeneDB ID: retro_ptro_271

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:226527476..226528286(+)
• Located in intron of: ENSPTRG00000024110

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRIM1
• Ensembl ID: ENSPTRG00000022987
• Aliases: None
• Description: DNA primase [Source:UniProtKB/TrEMBL;Acc:H2R0Q8]

Sequence

>retro_ptro_271
ATGAAAATGTCTGACCCCATCAAGCTGTCTGAGCTACTGAAATGTTATTACCAGAGGCTCTTTCCCTATTCTCTGTACTG
TAACTGGCTCAACTACAGCAGAGTGATAAAGAATTACTCCCAACACTGTGAATTTTCATTCACATTGAAAGATGACATTA
CATTCGATACCAATCCTTCAACAACCAGAGTGATCTGGAAAAGGAGATGCAGAAAATGAATCCATACAAGATTGATATAG
GTGCAGTATATTCCCACAGACCCAATCAACACAATACAGTGAAGCTGGGAGCTTTCCAGGCTCAGGAAAAAGAACTGGTG
TTTGACACTGACATGACAGACATGACAATGTGAGGAGATGCTGTAGTTCTGCAGATACATGTTCTAAGTGCTGGACCCTC
ATGACAAGGGCCATACGCATCACTGACACAGCACTGAAGGAGGACTTTGGATTTAAGCATTGTCTCTGGGTATATTCTGG
AAGGAGGGGTGTACATTGTTTGGTCTGTGATAAATCAGTTAGAAAACTGTCTTCGGTGGTATATTCTGGGATAGTTGAGT
ATTTGAGCCTTGTAAAGCGTGGTCAAGATGTTAAAAAGAAAGTTCACCTAACTGAAAAAATTCACCCTTTTGTCAGAAAA
TCTATAAACATAATTAAAAAAACTTTGAAGAATATGCCTTGGTTAATCAAGATATTCTCAAAAATAACAAAAGCTGGGAT
AAGATTTTAGCCCTTGTTCCTGAAACAATTCAGGATGAACTTCAACAAAGCTTCCAAAAGTCTCACAATTCACTTCAGCA
TTGGGAGCAC

Alignment

ORF - retro_ptro_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.4 %
• Parental protein coverage: 64.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  METFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDI-YIRYQSFNNQSDLEKE
          M...DP..L.ELLK.YY.RLFPYS.Y..WLNY..VIKNY.QH.EFSFTLKDDI.YIRYQSFNNQSDLEKE
Retrocopy MKMSDPIKLSELLKCYYQRLFPYSLYCNWLNYSRVIKNYSQHCEFSFTLKDDI<YIRYQSFNNQSDLEKE

Parental  MQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTD-YDDVRRCCSSADICPKCWTLMTMA
          MQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFD.DMTD..D.VRRCCSSAD.C.KCWTLMT.A
Retrocopy MQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDTDMTD<HDNVRRCCSSADTCSKCWTLMTRA

Parental  IRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKI
          IRI.D.ALKEDFGFKH.LWVYSGRRGVHC.VCD.SVRKLSS.V.SGIVEYLSLVK.GQDVKKKVHL.EKI
Retrocopy IRITDTALKEDFGFKHCLWVYSGRRGVHCLVCDKSVRKLSSVVYSGIVEYLSLVKRGQDVKKKVHLTEKI

Parental  HPFIRKSINIIK-KYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEH
          HPF.RKSINIIK.K.FEEYALVNQDIL.N..SWDKILALVPETI.DELQQSFQKSHNSLQ.WEH
Retrocopy HPFVRKSINIIK<KNFEEYALVNQDILKNNKSWDKILALVPETIQDELQQSFQKSHNSLQHWEH

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	2.90 RPM
SRP007412_cerebellum	0.11 RPM	8.17 RPM
SRP007412_heart	0.00 RPM	1.25 RPM
SRP007412_kidney	0.05 RPM	2.64 RPM
SRP007412_liver	0.03 RPM	3.37 RPM
SRP007412_testis	0.11 RPM	13.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_271 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_271 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_339
Pongo abelii	retro_pabe_356

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271 ,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352,