RetrogeneDB ID: retro_ptro_1478

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:30679840..30681132(-)
• Located in intron of: ENSPTRG00000013980

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMMT
• Ensembl ID: ENSPTRG00000012150
• Aliases: None
• Description: inner membrane protein, mitochondrial [Source:HGNC Symbol;Acc:6047]

Sequence

>retro_ptro_1478
GCCTCATATAAACTTCACAACACGATAGTTGATCTGGATAATGTGGTCAAAAAGGTCCAAGCAGCTCAATTTGAGGCTAA
GGTTGTATCTCAGTATCATGAGCTGGTGGGCCAAGCTCGGGATGACTTTAAACAACAGCTGGACAGTATTACTCCAGAAG
TCCTTCCTGGGTGGAAAGGAATGAGCGTTTTGGACCCAGCTGACAAGCTCTCTACTGATGATCTGAACTCCCTGATTGCC
CGTGCACATCGTCACATCGATCAGCTGAACAGAGAGCTAGCAGAACAGAAGGCCACAGAAAAGCAGCACATCACATTAGC
CTTGGAGAAACAAACGCTGGAAGAAAAGCGGGCATTTGACTTTGTAGTAGCAAAAGCATTAGAACATCATGGAAGTAAAA
TGCAGGCTGAATAGGACAGAAAGGTAGAGGAAGTCAGAGATGCCATGGAGAATGAAATGAGAACCTAGCTTCACTGACAG
GCAGCTGCCCACACTGATCACTTGCGAGATGTCCTTAGGGTTCAAGAACAGGAATTGAAGTATGAATTTGAGCAGAACCT
GTCTGAGAGACTCTCGGAACAAGAATTACAGTTTCGTCATCTCAGTCAAGAGCAAGTTCACAACTTTACTCTGGATATAA
ACACTGCCTATGCCAGACTCAGAGGAATCGAACACGCTGTTCAGAGTCATGCAGTTGCTGAAGAGGAAGCCAGAAAAGCC
TACCAACTCTGGCTTTCAGTGGAGGCATTAAAGTACAGCATGAAGACCTCATCTGCAGAAATGCCTACTGTCCCACTGGG
TAGTGCAGTTGAGGCCATCAAAGCCAACTGTTCTGATAATGAATTTACCAAAGCTTTAGCCACAGCTATCCCTCCAGAGT
CCCTGACCCATGGGGTGTACAGTGAAGAGACCCTTAGAGCCTGCTTTTATGCTGTTCAAAAACTGGCCCGAAGGGTAGCA
ATGATTGATTAAACCAGAAATAGCTTGTACCAGTACTTCTTCTCCTACCTGCAGTCCCTGCTTCTATTCCCGCCTCAGCA
ACTGAAGCTGCAGAGCTCTGATCTGAAGATATAAACACGTTTAAATTACTGTCATATGCCTCCTATTGCATTGAGCATGG
TGATCTGGAGCTAGTAGCAAAGTTTGTCAATCAGCTGAAGGGGGAATCCAGATGAGTGGCACAAGACTGGCTGAAGGAAG
CCTGAATAACCCTAGAAACGAAACAGATAGTGGAAATCCTGACAGCATATGCCAGCGCCGTAGGCACAAGAACCACTCAA
GTACAGCCAGAG

Alignment

ORF - retro_ptro_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 56.99 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEGKLHNMIVDLDNVVKKVQAAQSEAKVVSQYHELVVQARDDFKRELDSITPEVLPGWKGMSEYNLADKL
          A..KLHN.IVDLDNVVKKVQAAQ.EAKVVSQYHELV.QARDDFK..LDSITPEVLPGWKGMS....ADKL
Retrocopy ASYKLHNTIVDLDNVVKKVQAAQFEAKVVSQYHELVGQARDDFKQQLDSITPEVLPGWKGMSVLDPADKL

Parental  STDDLNSLIAHAHRRIDQLNRELAEQKATEKQHITLALEKQKLEEKRAFDSAVAKALEHHRSEIQAEQDR
          STDDLNSLIA.AHR.IDQLNRELAEQKATEKQHITLALEKQ.LEEKRAFD..VAKALEHH.S..QAE.DR
Retrocopy STDDLNSLIARAHRHIDQLNRELAEQKATEKQHITLALEKQTLEEKRAFDFVVAKALEHHGSKMQAE*DR

Parental  KIEEVRDAMENEMRTQLRRQAAAHTDHLRDVLRVQEQELKSEFEQNLSEKLSEQELQFRRLSQEQVDNFT
          K.EEVRDAMENEMRT.L..QAAAHTDHLRDVLRVQEQELK.EFEQNLSE.LSEQELQFR.LSQEQV.NFT
Retrocopy KVEEVRDAMENEMRT*LH*QAAAHTDHLRDVLRVQEQELKYEFEQNLSERLSEQELQFRHLSQEQVHNFT

Parental  LDINTAYARLRGIEQAVQSHAVAEEEARKAHQLWLSVEALKYSMKTSSAETPTIPLGSAVEAIKANCSDN
          LDINTAYARLRGIE.AVQSHAVAEEEARKA.QLWLSVEALKYSMKTSSAE.PT.PLGSAVEAIKANCSDN
Retrocopy LDINTAYARLRGIEHAVQSHAVAEEEARKAYQLWLSVEALKYSMKTSSAEMPTVPLGSAVEAIKANCSDN

Parental  EFTQALTAAIPPESLTRGVYSEETLRARFYAVQKLARRVAMIDETRNSLYQYFLSYLQSLLLFPPQQ-LK
          EFT.AL..AIPPESLT.GVYSEETLRA.FYAVQKLARRVAMID.TRNSLYQYF.SYLQS.LL..P.Q...
Retrocopy EFTKALATAIPPESLTHGVYSEETLRACFYAVQKLARRVAMID*TRNSLYQYFFSYLQS-LLLFPPQ<AT

Parental  PPPELCPEDINTFKLLSYASYCIEHGDLELAAKFVNQLKGESRRVAQDWLKEARMTLETKQIVEILTAYA
          ...EL..EDINTFKLLSYASYCIEHGDLEL.AKFVNQLKGESR.VAQDWLKEA..TLETKQIVEILTAYA
Retrocopy EAAEL*SEDINTFKLLSYASYCIEHGDLELVAKFVNQLKGESR*VAQDWLKEA*ITLETKQIVEILTAYA

Parental  SAVGIGTTQVQPE
          SAVG..TTQVQPE
Retrocopy SAVGTRTTQVQPE

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	48.90 RPM
SRP007412_cerebellum	0.00 RPM	47.64 RPM
SRP007412_heart	0.09 RPM	129.61 RPM
SRP007412_kidney	0.00 RPM	72.86 RPM
SRP007412_liver	0.00 RPM	32.44 RPM
SRP007412_testis	0.11 RPM	159.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1478 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1478 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2535
Gorilla gorilla	retro_ggor_1584

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132305	1 retrocopy	retro_hsap_2535,
Gorilla gorilla	ENSGGOG00000005264	1 retrocopy	retro_ggor_1584,
Pan troglodytes	ENSPTRG00000012150	1 retrocopy	retro_ptro_1478 ,