RetrogeneDB ID: retro_ptro_111

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:112381986..112383360(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005928
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000039565
• Aliases: None
• Description: None

Sequence

>retro_ptro_111
ATGGCTACGAGGGTGCTGAGCATGAGCGCCCGCCTGGGACCCGTGCCCCAGCCGCCGGCGCCGCAGGACGAGCCCGTGTT
CGCGCAGCTCAAGCCGGTGCTGGGCGCCGCGAATCCGGCCCGCGACGCGGCGCTCTTCCCCGGCGAGGAGCTGAAGCACG
CGCACCACCGCCCACAGGCGCAGCCCGCGCCCGCGCAGGCCCCGCAGCCGGCCCAGCCGCCCGCCACCGGCCCGCGGCTG
CCTCCAGAGGAGCTGGTCCAGACAAGATGTGAAATGGAGAAGTATCTGACACCTCAGCTTCCTCCAGTTCCTATAATTCC
AGAGCGTAAAAAGTATAGACGAGACAGTGCCTCAGTCATAGACCAGTTCTTCACTGACACTGAAGGGTTACCTTACAGTA
TCAACATGAACGTCTTCCTCCCTGACATCACTCACCTGAGAACTGGCCTCTACAAATCCCAGAGACCGTGCGTAACACAC
ATCAAGACAGAACCTGTTGCCATTTTCAGCCACCAGAGTGAAACAACTGCCCCTCCTCCGGCCCCGACCCAGGCCCTCCC
TGAGTTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGCACAATATTTTCATCAAACAAGAACTTCCTA
CACCAGATCTTCATCTTTCTGTCCCTACCCAGCAGGGCCACCTGTACCAGCTACTGAATACACCGGATCTAGATATGCCC
AGTTCTACAAATCAGACAGCAGCAATGGACACTCTTAATGTTTCTATGTCAGCTGCCATGGCAGGCCTTAACACACACAC
CTCTGCTGTTCCGCAGACTGCAGTGAAACAATTCCAGGGCATGCCCCCTTGCACATACACAATGCCAAGTCAGTTTCTTC
CACAACAGGCCACTTACTTTCCCCCGTCACCACCAAGCTCAGAGCCTGGAAGTCCAGATAGACAAGCAGAGATGCTCCAG
AATTTAACCCCACCTCCATCCTATGCTGCTACAATTGCTTCTAAACTGGCAATTCACAATCCAAATTTACCCACCACCCT
GCCAGTTAACTCACAAAACATCCAACCTGTCAGATACAATAGAAGGAGTAACCCCGATTTGGAGAAACGACGCATCCACT
ACTGCGATTACCCTGGTTGCACAAAAGTTTATACCAAGTCTTCTCATTTAAAAGCTCACCTGAGGACTCACACTGGTGAA
AAGCCATACAAGTGTACCTGGGAAGGCTGCGACTGGAGGTTCGCGCGATCGGATGAGCTGACCCGCCACTACCGGAAGCA
CACAGGCGCCAAGCCCTTCCAGTGCGGGGTGTGCAACCGCAGCTTCTCGCGCTCTGACCACCTGGCCCTGCATATGAAGA
GGCACCAGAACTGA

Alignment

ORF - retro_ptro_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 86.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRLPPEELVQTRCEMEKYLTPQLPPVPIIPEHKKYRRDSASVVDQFFTDTEGLPYSINMNVFLPDITHLR
          PRLPPEELVQTRCEMEKYLTPQLPPVPIIPE.KKYRRDSASV.DQFFTDTEGLPYSINMNVFLPDITHLR
Retrocopy PRLPPEELVQTRCEMEKYLTPQLPPVPIIPERKKYRRDSASVIDQFFTDTEGLPYSINMNVFLPDITHLR

Parental  TGLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEVNNIFIKQELPTPDL
          TGLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEV.NIFIKQELPTPDL
Retrocopy TGLYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEVHNIFIKQELPTPDL

Parental  HLSVPPQQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYT
          HLSVP.QQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYT
Retrocopy HLSVPTQQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYT

Parental  MPSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPV
          MPSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPV
Retrocopy MPSQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPV

Parental  RYNRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKH
          RYNRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKH
Retrocopy RYNRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKH

Parental  TGAKPFQCGVCNRSFSRSDHLALHMKRHQN
          TGAKPFQCGVCNRSFSRSDHLALHMKRHQN
Retrocopy TGAKPFQCGVCNRSFSRSDHLALHMKRHQN

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	0.05 RPM	0.97 RPM
SRP007412_cerebellum	0.07 RPM	0.68 RPM
SRP007412_heart	0.00 RPM	1.05 RPM
SRP007412_kidney	0.08 RPM	2.07 RPM
SRP007412_liver	0.03 RPM	0.36 RPM
SRP007412_testis	0.11 RPM	20.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_111 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009798	1 retrocopy	retro_chof_1208,
Callithrix jacchus	ENSCJAG00000021146	1 retrocopy	retro_cjac_3188,
Nomascus leucogenys	ENSNLEG00000016120	1 retrocopy	retro_nleu_65,
Pan troglodytes	ENSPTRG00000012850	1 retrocopy	retro_ptro_1948,
Pan troglodytes	ENSPTRG00000021957	1 retrocopy	retro_ptro_1104,
Pan troglodytes	ENSPTRG00000039565	2 retrocopies	retro_ptro_111 , retro_ptro_2968,