RetrogeneDB ID: retro_ptro_78

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:63239642..63240497(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041833
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CNOT8
• Ensembl ID: ENSPTRG00000017451
• Aliases: None
• Description: CCR4-NOT transcription complex subunit 8 [Source:RefSeq peptide;Acc:NP_001233465]

Sequence

>retro_ptro_78
ATGCCAGCGGCAACTGTAGATCATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACTTGGATGAAGAGATGAAGAAAAT
TCGTCAAGTTATCCGAAAATATAATTACGTTGCTATGGACACCGAGTTTCCAGGTGTGGTTGCAAGACCCATTGGAGAAT
TCAGGAGCAATGCTGACTATCAATACCAACTATTGCGGTGTAATGTAGACTTGTTAAAGATAATTCAGCTAGGACTGACA
TTTATGAATGAGCAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACGGAGGACAT
GTATGCCCAGGACTCTATAGAGCTACTAACAACATCTGGTATCCAGTTTAAAAAACATGAGGAGGAAGGAATTGAAACCC
AGTACTTTGCAGAACTTCTTATGACTTCTGGAGTGGTCCTCTGTGAAGGGGTCAAATGGTTGTCATTTCATAGCGGTTAT
GACTTTGGCTACTTAATCAAAATCCTAACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCGATT
GTTTTTTCCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAAAATCTCAAAGGTGGATTACAGGAGGTGGCAG
AACAGTTAGAGCTGGAACGGATAGGACCACAACATCAGGCAGGATCTGATTCACTGCTCACAGGAATGGCCTTTTTCAAA
ATGAGAGAAATGTTCTTTGAAGATCATATTGATGATGCCAAATATTGTGCTCATTTGTATGGCCTTTGTTCTGGTTCATC
CTATGTACAGAATGGCACAGGGAATGCATATGAAGAGGAAGCCAACAAGCAGTCA

Alignment

ORF - retro_ptro_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.07 %
• Parental protein coverage: 95.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPAALVENSQVICEVWASNLEEEMRKIREIVLSYSYIAMDTEFPGVVVRPIGEFRSSIDYQYQLLRCNVD
          MPAA.V..SQ.ICEVWA.NL.EEM.KIR.....Y.Y.AMDTEFPGVV.RPIGEFRS..DYQYQLLRCNVD
Retrocopy MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD

Parental  LLKIIQLGLTFTNEKGEYPSGINTWQFNFKFNLTEDMYSQDSIDLLANSGLQFQKHEEEGIDTLHFAELL
          LLKIIQLGLTF.NE.GEYP.G..TWQFNFKFNLTEDMY.QDSI.LL..SG.QF.KHEEEGI.T..FAELL
Retrocopy LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL

Parental  MTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEEEHEFFHILNLFFPSIYDVKYLMKSCKNLKGGLQ
          MTSGVVLC..VKWLSFHSGYDFGY..K.LT.S.LPEEE..FF.IL.LFFP.IYDVKYLMKSCKNLKGGLQ
Retrocopy MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ

Parental  EVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFFEDSIDDAKYCGRLYGLGTGVAQKQNEDVDSAQEK
          EVA.QL.L.RIG.QHQAGSDSLLTGMAFF.M.E.FFED.IDDAKYC..LYGL..G....QN.......E.
Retrocopy EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCAHLYGLCSGSSYVQNGTGNAYEEE

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	4.70 RPM	28.46 RPM
SRP007412_cerebellum	3.15 RPM	26.10 RPM
SRP007412_heart	2.19 RPM	16.06 RPM
SRP007412_kidney	3.84 RPM	25.63 RPM
SRP007412_liver	1.51 RPM	13.39 RPM
SRP007412_testis	5.06 RPM	58.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_78 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_78 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_78 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000020515	1 retrocopy	retro_mmus_3212,
Pan troglodytes	ENSPTRG00000017451	1 retrocopy	retro_ptro_78 ,