RetrogeneDB ID: retro_ptro_2306

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:155408764..155409452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIR1
• Ensembl ID: ENSPTRG00000012652
• Aliases: None
• Description: corepressor interacting with RBPJ, 1 [Source:HGNC Symbol;Acc:24217]

Sequence

>retro_ptro_2306
ATGGGGAAATCCTTCACCAACTTCATGTGCAAGAAGGATTTTCATCTTGCCTCCAAATCCAATATCAAAAAAGTATGGAT
GGCAGAACAGAAAATATCATATGATAAGAAGAAACAAGAATAATTAATGCAGCAATATCATAAAGAACAAGAATCATATG
ATAACAGATTGTTTATGGGAGATGAACGTGTAAATAATGGCCTTAATTTCATGTATGAAGCCCCACCAGGAGCTAAAAAA
GAAAACAAAGAGAAAAAAGAAACAGAAAGAGAGACTGAATACAAATGTGAATGGCAGAAAGGAGCCCCACGAGAAAAATA
TGTCAAAGATGACATGAACATCAGAGAGCAGCCCTGTGGTATTGAGGTTTGAAATGTGTGGTGCATTAAATGTCACCAAT
GGGATCATGTCAACACAGATCAAGAACGTCCTTTGTTTGGTCTTTCTGGAATCAATGCAAGTTTGGTTCCCACTGATGGC
TCAGGACCATCGATGCACCCCTTGGAGCTAATAGCGAAGATGAGAAACAGTGGGTTTGCACTGAACCGAAATGTACTGGG
GAGAACCTGACCGCAAATGATCCATCAAAGGAGTATGTTGCAAGTGAGGGTGAAGAATATCCAGAAGTTGAATGTTTAAA
GTCACTAGCAGCTAAACAAAAACAGAAATTTTCAGGAAATTAGATCGA

Alignment

ORF - retro_ptro_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
          MGKSF.NFMCKKDFH.ASKSNIKKVWMAEQKISYDKKKQE.LMQQY.KEQESYDNRL.MGDERV.NGLNF
Retrocopy MGKSFTNFMCKKDFHLASKSNIKKVWMAEQKISYDKKKQE*LMQQYHKEQESYDNRLFMGDERVNNGLNF

Parental  MYEAPPGAKKGTSSKEETEGETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNTD
          MYEAPPGA..............EYK.EWQKGAPREKY.KDDMNIR.QP.GI.V.NV.CIKCH.W.HVNTD
Retrocopy MYEAPPGAXXXXXXXXXXXXXXEYKCEWQKGAPREKYVKDDMNIREQPCGIEV*NVWCIKCHQWDHVNTD

Parental  RECPLFGLSGINASSVPTDGSGPSMHPSELIAEMRNSGFALKRNVLGR-NLTANDPSQEYVASEGEEDPE
          .E.PLFGLSGINAS.VPTDGSGPSMHP.ELIA.MRNSGFAL.RNVLGR.NLTANDPS.EYVASEGEE.PE
Retrocopy QERPLFGLSGINASLVPTDGSGPSMHPLELIAKMRNSGFALNRNVLGR<NLTANDPSKEYVASEGEEYPE

Parental  VEFLKSLTTKQKQK-LLRKLDR
          VE.LKSL..KQKQK...RKLDR
Retrocopy VECLKSLAAKQKQK<IFRKLDR

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	0.09 RPM	18.04 RPM
SRP007412_cerebellum	0.25 RPM	33.81 RPM
SRP007412_heart	0.55 RPM	23.58 RPM
SRP007412_kidney	0.26 RPM	22.15 RPM
SRP007412_liver	0.20 RPM	16.37 RPM
SRP007412_testis	1.48 RPM	105.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2306 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2306 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3394

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007884	1 retrocopy	retro_cjac_2152,
Homo sapiens	ENSG00000138433	2 retrocopies	retro_hsap_3082, retro_hsap_3394,
Macaca mulatta	ENSMMUG00000023006	1 retrocopy	retro_mmul_1967,
Mustela putorius furo	ENSMPUG00000013943	1 retrocopy	retro_mputfur_178,
Mus musculus	ENSMUSG00000041777	2 retrocopies	retro_mmus_2064, retro_mmus_3104,
Nomascus leucogenys	ENSNLEG00000005869	3 retrocopies	retro_nleu_1540, retro_nleu_2013, retro_nleu_2691,
Pan troglodytes	ENSPTRG00000012652	2 retrocopies	retro_ptro_2079, retro_ptro_2306 ,