RetrogeneDB ID: retro_ptro_7

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:36732530..36733544(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005793
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSNK1E
• Ensembl ID: ENSPTRG00000014365
• Aliases: None
• Description: None

Sequence

>retro_ptro_7
ATGGCAAACAACAGCGGCTCCAAAGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC
CTTTGGAGACGTTTATCTGGGCATCACCACCACCAACGGCGAGGAAGTAGCAGTGAAGCTGGAATCTCAGAAAGTCAAGC
ACCCCCAGTTGCTGTATGAGAGCAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT
CAGGAAAAAGACAACAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG
GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTAC
ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA
TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT
TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAGGGCTATGACAAAAAAACAAAAATATGAAAAGATTAGTGAGAAGAAG
GTGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG
CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT
ACACATTTGATTGGACGATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA
ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAAGATAACTAA

Alignment

ORF - retro_ptro_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.81 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRVGNKYRLGRKIGSGSFGDIYLGANIASGEEVAIKLECVKTKHPQLHIESKFYKMMQGGVGIPSIKWC
          EL.VG.KY.L.RKIGSGSFGD.YLG.....GEEVA.KLE..K.KHPQL..ESK.Y...QGGVGIP...W.
Retrocopy ELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEEVAVKLESQKVKHPQLLYESKLYTILQGGVGIPHMHWY

Parental  GAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKK
          G.E.D.NV.VM.LLGPSLEDLFNFCSR.F..KTVL.LADQMISRIEY.H.KNF.HRD.KPDNFLMG.G..
Retrocopy GQEKDNNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPDNFLMGTGRH

Parental  GNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSL
          .N....IDFGLAKKYRD.RT.QHIPYRE.K.L.GT.RYASIN.HLGIEQSRRDD.ESLGYV.MYFN..SL
Retrocopy CNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYVFMYFNRTSL

Parental  PWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFSTYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQG
          PWQGL.A.TK.QKYE.ISEKK.STP.EVLCKG.P.EF..YLN.CR.LRF...PDY.YLRQLFR.LF....
Retrocopy PWQGLRAMTKKQKYEKISEKKVSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQLFRILFRTLN

Parental  FSYDYVFDWNMLKFGAAR
          ..YDY.FDW.MLK..AA.
Retrocopy HQYDYTFDWTMLKQKAAQ

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	0.07 RPM	121.94 RPM
SRP007412_cerebellum	0.14 RPM	131.96 RPM
SRP007412_heart	0.00 RPM	52.14 RPM
SRP007412_kidney	0.05 RPM	47.47 RPM
SRP007412_liver	0.00 RPM	26.15 RPM
SRP007412_testis	9.27 RPM	16.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_7 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_7 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_7 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_32
Gorilla gorilla	retro_ggor_984
Pongo abelii	retro_pabe_170
Macaca mulatta	retro_mmul_295
Callithrix jacchus	retro_cjac_2680

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000011583	1 retrocopy	retro_mmur_10,
Nomascus leucogenys	ENSNLEG00000015080	1 retrocopy	retro_nleu_117,
Pongo abelii	ENSPPYG00000011818	1 retrocopy	retro_pabe_170,
Pan troglodytes	ENSPTRG00000014365	1 retrocopy	retro_ptro_7 ,