RetrogeneDB ID: retro_ptro_3183

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:9734911..9735958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSPTRG00000006753
• Aliases: None
• Description: None

Sequence

>retro_ptro_3183
TACATTGTGAATGGATCTCAGGAGGCCAATAAGCTGCAAGACATATTGGATGGACTCATTAAAAAATTTGTTCTCTGTCC
TGAATGTGAGAATCCTGAAACAGATATGCATGTCAAGCCAAAGCAGCAAACAATAGGTAATTCTTATAAAGCCTGTGGCT
ATCGAGGCATGCTTGACACACATCATAAACTCTGCACATTCATTCTCAAAAACCCACCTGAGAACAGTGACAGTGGTACA
GGAAAGAAAGAAAAGGAAAAGAAAAATATAAAGGGCAAAGACAAGGAAAATGGCTCCGTATCCAGCAGTGAGACACCACC
ACCAAAGAAATTAGCCCTACTCCACATACAGTGGAAGAAGAGGAGGATGACTGGGGGGAAGATACAACTGAGGAAGCTCA
AAGGTGCAGAATGGATGAAATCAGTGATCATGCAAAAGTTCTGATACTCCATGATGATTTGGAAAAAACAGTCGAGGAGC
GGGCCAACATCCTGTTTGATTTTGGAAGAAAAAGAAAGAAGAGGGTACCATTGATTTATGTGACAAAGAAATTGTTACTG
AAGCAAAGGACTGGATGTTAAAGCCTTGGGCCCTCTTGTTCTGACTGCATTCTTTTTAAAGAGGAGATTAAGAACACATA
AGAAATACAGGCACCATTTCTTATGATTTTGTCACAACAACAAAAAAGCTCAATGGTACCTTCTTCATGGCTTTACGTGT
GGGGTAGCAATGCACCAAGCTCAGCTTATCTCTAAGATTCCAAATATCTTGAAGGAGATGTATGATGTAGATTTTTTAGA
AGAAGAGGTCGTCATCAGCTGGTCGGAAAAAGGCCTTTAAGAAACATGTCTCAAAAGAACTTGCCAAAGAGATTCGTGTC
AAAGTAGAACCATTTATAAAATGAAGGAGGCAGAGGAAGAATCTTCTGGTGGTGAAGAAGATGAAGATGAGAACATTGAG
GTGGTGTATTAGAAGACTGCCAGTGTACCTAAAGTTGAAACTGTAAAGTCCAACAACAAGGATGATGACATTGATATTGA
TGCCATT

Alignment

ORF - retro_ptro_3183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 83.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YIVNGSHEANKLQDMLDGFIKKFVLCPECENPETDLHVNPKKQTIGNSCKACGYRGMLDTHHKLCTFILK
          YIVNGS.EANKLQD.LDG.IKKFVLCPECENPETD.HV.PK.QTIGNS.KACGYRGMLDTHHKLCTFILK
Retrocopy YIVNGSQEANKLQDILDGLIKKFVLCPECENPETDMHVKPKQQTIGNSYKACGYRGMLDTHHKLCTFILK

Parental  NPPENSDSGTGKKEKEKKNRKGKDKENGSVSSSETPPPPPPPN-EINPPPHTMEEEEDDDWGEDTTEEAQ
          NPPENSDSGT.................GSVSSSET....PPP..EI.P.PHT.EEEEDD.WGEDTTEEAQ
Retrocopy NPPENSDSGTXXXXXXXXXXXXXXXXXGSVSSSET----PPPK<EISPTPHTVEEEEDD-WGEDTTEEAQ

Parental  RRRMDEISDHAKVLTLSDDLERTIEERVNILFDFV-KKKKEEGVIDSSDKEIVAEAER-LDVKAMGPLVL
          R.RMDEISDHAKVL.L.DDLE.T.EER.NILFDF..KKKKEEG.ID..DKEIV.EA...LDVKA.GPLVL
Retrocopy RCRMDEISDHAKVLILHDDLEKTVEERANILFDFG<KKKKEEGTIDLCDKEIVTEAKD<LDVKALGPLVL

Parental  TEVLFNEKIREQIKKYRRHFLRFCHNNKKAQRYLLHGLECVVAMHQAQLISKIPHILKEMYDADLLEEEV
          T........R...KKYR.HFL.FCHNNKKAQ.YLLHG..C.VAMHQAQLISKIP.ILKEMYD.D.LEEEV
Retrocopy TAFFLKRRLRTH-KKYRHHFL*FCHNNKKAQWYLLHGFTCGVAMHQAQLISKIPNILKEMYDVDFLEEEV

Parental  IISWSE-KASKKYVSKELAKEIRVKAEPFIKWLKE-AEEESSGGEEEDEDENIEVVYSKTASVPKVETVK
          .ISWSE.KA.KK.VSKELAKEIRVK.EPFIK......EE.S.G..EEDEDENIEVVY.KTASVPKVETVK
Retrocopy VISWSE>KAFKKHVSKELAKEIRVKVEPFIK*RRQ<EEESSGG--EEDEDENIEVVY*KTASVPKVETVK

Parental  SDNKDDDIDIDAI
          S.NKDDDIDIDAI
Retrocopy SNNKDDDIDIDAI

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	132.49 RPM
SRP007412_cerebellum	0.07 RPM	180.64 RPM
SRP007412_heart	0.06 RPM	129.29 RPM
SRP007412_kidney	0.03 RPM	178.02 RPM
SRP007412_liver	0.07 RPM	185.90 RPM
SRP007412_testis	0.42 RPM	524.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3183 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3183 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4782
Pongo abelii	retro_pabe_3722

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Homo sapiens	ENSG00000100664	1 retrocopy	retro_hsap_4782,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Nomascus leucogenys	ENSNLEG00000016105	1 retrocopy	retro_nleu_1102,
Pongo abelii	ENSPPYG00000006169	1 retrocopy	retro_pabe_3722,
Pan troglodytes	ENSPTRG00000006753	1 retrocopy	retro_ptro_3183 ,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,