RetrogeneDB ID: retro_ptro_67

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:22500691..22501969(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000028314
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CBLL1
• Ensembl ID: ENSPTRG00000019583
• Aliases: None
• Description: None

Sequence

>retro_ptro_67
ATGAACAAGATGCCTGCTGGTGAACGAGAATGTGAATATAACAAAGAAGGGAAGTACTACACTAAAGGAGTTAAACTGGT
GAGAAAAAAGAACAAAATTCCTGGTTACCGTTGGGGGGACATTAAGATAAACCTCATAGGTGAAAAGGATGATTTACCAA
TTCATTTCTGTGACAAATGTGATTTGCCTATTAAAATCTATGGGCGAATAATTCCATGCAAGCATGCTTTTTGCTATGAC
TGTGCTGATTTATATGACAAAGTCGGATATAAAGTATGTCCACGCTGTCGTTATCCTGTGCTGCGAATTGAGGCGCATAA
ACGAGGTTTTGTCTTCATGTGTAGTATTGTTCAGCAGTGCAAGAGAACATACTTGTCTCAGAAAAGCTTACAGGCTCATA
TCAAACGCCGCCATAAGAGAGCTCGAAAACAAGTTACCAGCGCTTCGCTTGAAAAAGTTCGTCCTCATATTGCTCCGCCA
CAAACTGAAATCTCTGAAATCCCTAAAAGACTGCAAGACAGGGACCATCTAAGCTATATTCCACCACAGCAGCACACCAT
GGTGTCACTACCGTCTGTGCAACATATGCTACACGAGCAACATAATCAGCCACATAAGGATATTCAGGCTCCTCCCCCAG
AACTATCTCTAAGTCTGCCTTTTCCCATCCAGTGGGAAACCGTTAGTATTTTTACGAGAAAACATGGCAATTTAACAGTT
GATCATATTCAGAATAACTCAGATTCTGGTGCTGAGAAGCCAACACCTCCCGACTATTATCCTGAGTATCAAAGTCAACC
AGCGGTATCGTCCCCTCATCATATTATACCTCAGAAACAGCATTATGCGCCACCTCCATCTCCATCATCACCAGTAAACC
ATCAAATGCCATATCCTCCTCAGGATGTAGTTACTCCTAACTCGGTTCGTAGCCAAGTGCCAGCTCTAACCACGACCTAC
GATCCATCATCTGGATATAGTATTGTAAAGGTGCCACCTGATACGAATTCTCCTCCACTACGTGCTCCCCAGTCTCAAAA
TGGTAATCCATCTGCAAGTGAATTTGCTTCTCACCATTATAACCTTAACTTTTTACCTCAGTTCACCGAAAATCAAGAAA
CCTTGAGCCCTCAGTTTACACAAACAGATGCAATGGATCATAGAAGATGGCCTGCATGGAAACGACTGTCACCTTGTCCA
CCAACGCGGAGTCCACCTCCTTCAACCCTACATGGTCGATCACATCATTCATACCAGAGAAGACATAGACGGTATTAA

Alignment

ORF - retro_ptro_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.74 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KAPPGDEEGFDYNEEERYDCKGGELFANQRRFPGHLFWDFQINILGEKDDTPVHFCDKCGLPIKIYGRMI
          K.P.G..E...YN.E..Y..KG..L.......PG....D..IN..GEKDD.P.HFCDKC.LPIKIYGR.I
Retrocopy KMPAGERE-CEYNKEGKYYTKGVKLVRKKNKIPGYRWGDIKINLIGEKDDLPIHFCDKCDLPIKIYGRII

Parental  PCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRA
          PCKH.FCYDCA.L..K.G.K.CP.C..PV.RIE...RG..FMCSIVQ.CKRTYLSQ..LQAHI..RH.RA
Retrocopy PCKHAFCYDCADLYDKVGYKVCPRCRYPVLRIEAHKRGFVFMCSIVQQCKRTYLSQKSLQAHIKRRHKRA

Parental  GKPVTRASLENVHPPIAPPPTEIPERFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRAP
          .K.VT.ASLE.V.P.IAPP.TEI.E......D..H.S.IPP.QH.M...P..QH..HE..NQPH.DI.AP
Retrocopy RKQVTSASLEKVRPHIAPPQTEISEIPKRLQDRDHLSYIPPQQHTMVSLPSVQHMLHEQHNQPHKDIQAP

Parental  PAELSMAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQP--VVSHP
          P.ELS...P.P.....ET..I.TRKH.NL....IQ..S.SGA..P.PP...P..........P.......
Retrocopy PPELSLSLPFP--IQWETVSIFTRKHGNLTVDHIQNNSDSGAEKPTPPDYYPEYQSQPAVSSPHHIIPQK

Parental  HHIMPPQQHYAP
          .H..PP.....P
Retrocopy QHYAPPPSPSSP

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	0.00 RPM	16.89 RPM
SRP007412_cerebellum	0.00 RPM	32.01 RPM
SRP007412_heart	0.00 RPM	19.24 RPM
SRP007412_kidney	0.00 RPM	14.72 RPM
SRP007412_liver	0.03 RPM	13.49 RPM
SRP007412_testis	34.88 RPM	82.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_67 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_67 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_67 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_49
Gorilla gorilla	retro_ggor_164
Pongo abelii	retro_pabe_112
Canis familiaris	retro_cfam_2047

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016379	1 retrocopy	retro_cjac_4046,
Homo sapiens	ENSG00000105879	1 retrocopy	retro_hsap_49,
Gorilla gorilla	ENSGGOG00000004921	1 retrocopy	retro_ggor_164,
Microcebus murinus	ENSMICG00000012936	1 retrocopy	retro_mmur_1635,
Nomascus leucogenys	ENSNLEG00000008660	1 retrocopy	retro_nleu_19,
Pongo abelii	ENSPPYG00000017904	1 retrocopy	retro_pabe_112,
Pan troglodytes	ENSPTRG00000019583	1 retrocopy	retro_ptro_67 ,
Rattus norvegicus	ENSRNOG00000007253	1 retrocopy	retro_rnor_1063,