RetrogeneDB ID: retro_ptro_871

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:64670387..64671386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGMN
• Ensembl ID: ENSPTRG00000006655
• Aliases: None
• Description: None

Sequence

>retro_ptro_871
GACTATACTGGAGAGGATGTTACCCCACAAAATTTCCTTGCTGTGTTGACAGGCGATGCAGAAGCAGTGAAGGGCATAGG
AACCGGGAAAGTCCTGAAGAGCGGTCCCCAGGATCATGTATGTGTTCGTTTACTTCACTGACCATGGATCTACTGGAATA
CTGGTTTTTCCCAATGAAGATCTTCATGTAAAGTACCTGAATGAGACCATCCATTACATGTACATACATAAAATGTACCA
AAAGATGGTGTTCTATATTGAAGCCTGTGAGTCTGGGTCCATGATGAACCACCTGCCTGGTGATACTAATGTTTATGCAA
CTACTACTGCCAACCCCAGAGAGTCGTCCTACACCTGTTACTATGATGAGAAGAGGTCGACGTACCTGGGGGACTGGTAC
AGCGTCAACTGGATGGAAGACTCAGACGTGGAAGATCTGACTAACCAGACGCTGCACAAGCAGTACCACCTGGTAAAATC
ACACACCAATACCAGCCACATCATGCAGTACGGAAACGAAACGATCTCCACATTAAAGTGATGCAGTTTCAGAGTATGAA
ACACAAAGCCAGTTCTCCTATCTCCCTGCCTCCAGTCACACCCCTTGACCTCACCCCCAGCCCTGAGGTGCCCCTCATGA
TCGTGAAAAGGAAACTGATGAACACCAACGATCTAGAGGACTCCAGGCAGCTCACAGAGGAGATCCAGCGGCATCTGGAT
GCCAGGCACCTCATTGAGAAGTCAGTGCGCAAGATCGCCTCCTTGCTGGCAGCGTCCGAGGCTGAGGCGGAGCAGCTCCT
GTCTGAGAGAGCCCCGTTCACGGGGCATAGCTGCTACCTGGAGGCCCTGCTGCACTTCCAGACCCACTGCTTCAACTGGC
ACTCCCCCACGTGCGAGTATGCGTTGAGACATTTGTACGTGCTGGCCAACCTTTGTGAGAAACCGTATCCGCTTCACAGG
ATAAAATTGTCCATGGACCACGTGTGCGTCGGTCGCTAC

Alignment

ORF - retro_ptro_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.46 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYTGEDVTPQNFLAVLRGDAEAVKGIGS-GKVLKSGPQD-HVFIYFTDHGSTGILVFPNEDLHVKDLNET
          DYTGEDVTPQNFLAVL.GDAEAVKGIG..GK.....P....VF.YFTDHGSTGILVFPNEDLHVK.LNET
Retrocopy DYTGEDVTPQNFLAVLTGDAEAVKGIGT>GKS*RAVPRIMYVFVYFTDHGSTGILVFPNEDLHVKYLNET

Parental  IHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWME
          IHYMY.HKMY.KMVFYIEACESGSMMNHLP...NVYATT.ANPRESSY.CYYDEKRSTYLGDWYSVNWME
Retrocopy IHYMYIHKMYQKMVFYIEACESGSMMNHLPGDTNVYATTTANPRESSYTCYYDEKRSTYLGDWYSVNWME

Parental  DSDVEDLTKETLHKQYHLVKSHTNTSHVMQYGNKTISTMK-VMQFQGMKHKASSPISLPPVTHLDLTPSP
          DSDVEDLT..TLHKQYHLVKSHTNTSH.MQYGN.TIST.K.VMQFQ.MKHKASSPISLPPVT.LDLTPSP
Retrocopy DSDVEDLTNQTLHKQYHLVKSHTNTSHIMQYGNETISTLK<VMQFQSMKHKASSPISLPPVTPLDLTPSP

Parental  DVPLTIMKRKLMNTNDLEESRQLTEEIQRHLDARHLIEKSVRKIVSLLAASEAEVEQLLSERAPLTGHSC
          .VPL.I.KRKLMNTNDLE.SRQLTEEIQRHLDARHLIEKSVRKI.SLLAASEAE.EQLLSERAP.TGHSC
Retrocopy EVPLMIVKRKLMNTNDLEDSRQLTEEIQRHLDARHLIEKSVRKIASLLAASEAEAEQLLSERAPFTGHSC

Parental  YPEALLHFRTHCFNWHSPTYEYALRHLYVLVNLCEKPYPLHRIKLSMDHVCLGHY
          Y.EALLHF.THCFNWHSPT.EYALRHLYVL.NLCEKPYPLHRIKLSMDHVC.G.Y
Retrocopy YLEALLHFQTHCFNWHSPTCEYALRHLYVLANLCEKPYPLHRIKLSMDHVCVGRY

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	39.22 RPM
SRP007412_cerebellum	0.00 RPM	34.31 RPM
SRP007412_heart	0.00 RPM	53.95 RPM
SRP007412_kidney	0.13 RPM	343.48 RPM
SRP007412_liver	0.16 RPM	302.01 RPM
SRP007412_testis	0.00 RPM	20.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_871 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_871 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1272

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100600	1 retrocopy	retro_hsap_1272,
Pan troglodytes	ENSPTRG00000006655	1 retrocopy	retro_ptro_871 ,