RetrogeneDB ID: retro_ptro_1649

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:144924891..144925560(+)
• Located in intron of: ENSPTRG00000012508

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSPTRG00000006976
• Aliases: None
• Description: leucine rich repeat containing 57 [Source:HGNC Symbol;Acc:26719]

Sequence

>retro_ptro_1649
ATAGGAAATGGTGCCCTCGGTACTCAAGTGGAATGGGCATACTAAACTGGTGTCTCCCAGTTTAAGGACCATGGGCTGAC
CAAGTTCTCCTTAGAATTGTAGACACTAATGAGCAATCCCAGGACCATCAATTTGTCCAACAACAAGATGGACAACCTAC
CACTTTTGCTGATACAAAAGTTCACTCTGCTGAAGAACCTCCCCCTGAACAACATAAACTGGTCTGCCTAATGAGATTAT
GCAATCCTAAAAAAATTCTAGAGATGCTACGCCTAAACGGCAGTCACCTGAGAGAGCTGCCATCTACCTTTGGGCAACTC
TCTACCCTCAAGACCCTGAGCCTCTCTGGGAACCAACTGGGAGCACTATCACCCAACTTTGTAGCCTAGGCCACCAGATG
TGGTGGATCTTTCCAAGAACCAGATTTGAAGTATACCTGACATAGCAGGAGAGCTGCAGGTCATCAAACTTATCCTCAAC
TGGAAGAAGATATATCAGGTCTCAATAAAGATATCTGGCTGTCCTTGCCTTAAAATTCTTCACCTGGAAGAGAACTGTCT
TGAGCTCAGCATGCTTTCACAGGGCATCTGCAGTGATTGCCAGATCTGTCCACTTGATATGGAAGGTAATCTTTTTAAAA
TAAACTTCAATAAGTACATGGAGAGGTTC

Alignment

ORF - retro_ptro_1649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 93.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLKDRGLTEFPADLQKLTSNLRTIDLSNNKIESLPPLLIGKFTLLKSLSLN
          .GN.AL...VE.A..TGV.Q.KD.GLT.F...L..L.SN.RTI.LSNNK...LP.LLI.KFTLLK.L.LN
Retrocopy IGNGALGTQVEWAY*TGVSQFKDHGLTKFSLEL*TLMSNPRTINLSNNKMDNLPLLLIQKFTLLKNLPLN

Parental  N-NKLTVLPDEICNLKK-LETLSLNNNHLRELPSTFGQLSALKTLSLSGNQLGALPP-QLCSLRHL-DVM
          N..KL..L....CN.KK.LE.L.LN..HLRELPSTFGQLS.LKTLSLSGNQLGAL.P.QLCSL.H..DV.
Retrocopy N<HKLVCLM-RLCNPKKILEMLRLNGSHLRELPSTFGQLSTLKTLSLSGNQLGALSP<QLCSLGHQ<DVV

Parental  DLSKNQIRSIPDSVGELQVIELNLNQNQISQISVKISCCPRLKILRLEENCLELSMLPQSILSDSQICLL
          DLSKNQI.SIPD..GELQVI.L.LN...I.Q.S.KIS.CP.LKIL.LEENCLELSML.Q.I.SD.QIC.L
Retrocopy DLSKNQI*SIPDIAGELQVIKLILNWKKIYQVSIKISGCPCLKILHLEENCLELSMLSQGICSDCQICPL

Parental  AVEGNLFEIKKLRELEGY
          ..EGNLF.I......E..
Retrocopy DMEGNLFKINFNKYMERF

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	9.24 RPM
SRP007412_cerebellum	0.00 RPM	6.70 RPM
SRP007412_heart	0.00 RPM	6.50 RPM
SRP007412_kidney	0.00 RPM	8.05 RPM
SRP007412_liver	0.00 RPM	3.93 RPM
SRP007412_testis	0.00 RPM	5.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1649 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1649 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000002325	1 retrocopy	retro_ptro_425,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649 , retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,