RetrogeneDB ID: retro_ptro_2968

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389087.1:7278..8412(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ptro_2968
CTGCCTCCAGAGGAGCTGGTCCAGACAAGATGTGAAATGGGGAAGTATCTGACACCTCAGCTTCCTCCAGTTCCTATAAT
TCCAGAGCATAAAAAGTATAGACGAGACAGCGCCTCAGTCGTAGACCAGTTCTTCACTGACACTGAAGGGTTACCTTACA
GTATCAACATGAACGTCTTCCTCCCTGACATCACTCACCTGAGAACTGGCCTCTACAAATCCCAGAGACCGTGCGTAACA
CACATCAAGACAGAACCTGTTGCCATTTTCAGCCACCAGAGTGAAACAACTGCCCCTCCTCCGGCCCCGACCCAGGCCCT
CCCTGAGTTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGCACAATATTTTCATCAAACAAGAACTTC
CTACACCAGATCTTCATCTTTCTGTCCCTACCCAGCAGGGCCACCTGTACCAGCTACTGAATACACCGGATCTAGATATG
CCCAGTTCTACAAATCAGAGAGCAGCAATGGACACTCTTAATGTTTCTATGTCAGCTGCCATGGCAGGCCTTAACACACA
CACCTCTGCTGTTCCGCAGACTGCAGTGAAACAATTCCAGGGCATGCCCCCTTGCACATACACAATGCCAAGTCAGTTTC
TTCCACAACAGGCCACTTACTTTCCCCCGTCACCACCAAGCTCAGAGCCTGGAAGTCCAGATAGACAAACAGAGATGCTC
CAGAATTTAACCGCACCTCCATCCTATGCTGCTACAATTGCTTCTAAACTGGCAATTCACAATCCAAATTTACCCACCAC
CCTGCCAGTTAACTCACAAAACATGCAACCTGTCAGATACAATAGAAGGAGTAACCCCGATTTGGAGAAACGACGCATCC
ACTACTGCGATTACCCTGGTTGCACAAAAGTTTATACCAAGTCTTCTCATTTAAAAGCTCACCTGAGGACTCACACTGGT
GAAAAGCCATACAAGTGTACCTGGGAAGGCTGCGACTGGAGGTTCGCGTGATCGGATGAGCTGACCCGCCACTACCGGAA
GCACACAGGCGCCAAGCCCTTCCAGTGCGGGGTGTGCAACCGCAGCTTCTCGCGCTCTGACCACCTGGCCCTGCATATGA
AGAGGCACCAGAAC

Alignment

ORF - retro_ptro_2968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.88 %
• Parental protein coverage: 86.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPPEELVQTRCEMEKYLTPQLPPVPIIPEHKKYRRDSASVVDQFFTDTEGLPYSINMNVFLPDITHLRTG
          LPPEELVQTRCEM.KYLTPQLPPVPIIPEHKKYRRDSASVVDQFFTDTEGLPYSINMNVFLPDITHLRTG
Retrocopy LPPEELVQTRCEMGKYLTPQLPPVPIIPEHKKYRRDSASVVDQFFTDTEGLPYSINMNVFLPDITHLRTG

Parental  LYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEVNNIFIKQELPTPDLHL
          LYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEV.NIFIKQELPTPDLHL
Retrocopy LYKSQRPCVTHIKTEPVAIFSHQSETTAPPPAPTQALPEFTSIFSSHQTAAPEVHNIFIKQELPTPDLHL

Parental  SVPPQQGHLYQLLNTPDLDMPSSTNQTAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYTMP
          SVP.QQGHLYQLLNTPDLDMPSSTNQ.AAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYTMP
Retrocopy SVPTQQGHLYQLLNTPDLDMPSSTNQRAAMDTLNVSMSAAMAGLNTHTSAVPQTAVKQFQGMPPCTYTMP

Parental  SQFLPQQATYFPPSPPSSEPGSPDRQAEMLQNLTPPPSYAATIASKLAIHNPNLPTTLPVNSQNIQPVRY
          SQFLPQQATYFPPSPPSSEPGSPDRQ.EMLQNLT.PPSYAATIASKLAIHNPNLPTTLPVNSQN.QPVRY
Retrocopy SQFLPQQATYFPPSPPSSEPGSPDRQTEMLQNLTAPPSYAATIASKLAIHNPNLPTTLPVNSQNMQPVRY

Parental  NRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTG
          NRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFA.SDELTRHYRKHTG
Retrocopy NRRSNPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFA*SDELTRHYRKHTG

Parental  AKPFQCGVCNRSFSRSDHLALHMKRHQN
          AKPFQCGVCNRSFSRSDHLALHMKRHQN
Retrocopy AKPFQCGVCNRSFSRSDHLALHMKRHQN

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	0.73 RPM	0.97 RPM
SRP007412_cerebellum	1.25 RPM	0.68 RPM
SRP007412_heart	0.15 RPM	1.05 RPM
SRP007412_kidney	0.29 RPM	2.07 RPM
SRP007412_liver	0.26 RPM	0.36 RPM
SRP007412_testis	0.21 RPM	20.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2968 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2968 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 ,