RetrogeneDB ID: retro_pabe_112

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:22338142..22339420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020184
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CBLL1
• Ensembl ID: ENSPPYG00000017904
• Aliases: None
• Description: Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21225]

Sequence

>retro_pabe_112
ATGAACAAGATGCCTGCTGGTAAACAAGAATGTGAATATAACAAAGAAGGGAAGTACTACTCTAAAGGAGTTAAACTGGT
GAGAAAAAAGAAAAAAATTCCTGGTTACCATTGGGGGGACATTAAGATAAACATCATAGGTGAAAAGGATGATTCACCAA
TTCATTTCTGTGACAAATGTGATTTGCCTATTAAAATCTATGGGCGAATAATTCCATGCAAGCATGCTTTTTGCTATGAC
TGTGCTAATTTAGATGACAAAATCGGATATAAAATATGTCCACGCTGTCGTTATCCCGTGCTGCGAATTGAGGAGCATAA
ACGAGGTTCTGTCTTCATGTGTAGTGTTGTTCCGCAATGCAAGAGAACATACTTGTCTCAGAAAAGCCTACAGGCTCACA
TCAAACGCCGCCATAAGAGAGCTCGAAAACAAGTTACCAGCGCTTCGCTTGAAAAAGTTCGTCCTCATATTGCTCCGCCA
CGAACTGAAATCTCTGAAATCCCTAAAAGACTGCTAGACAGGGACCATCTAAGCTATATTCCACCAGAGCAGCACACTAT
GATGTCACTACCGTCTGTGCAACATATGCTACACGAGCAACATAATCAGCCACATAAGGCTATTCAGGCTCCTCCTCCAG
AACTATCTCTAAGTCCGCCTTTTCCCATCCAGTGGGAAACCGTTAGTATTTTTACGAGAAAACACGGCAATTTAACAGTT
GATCATATTCAGAATAACTCAGATTCTGGTGTTAAGAAGCCAACACCTCCTGACCATCATCCTGAGTATCAAAGGCAACC
AGCGGTATCGTCCCCTCATCATATTATACCTCAGAAACAGCGTTATGCACCACCTCCATCTCCATCATTACCAGTAAACC
ATCCAATGCCATATCCTCCTCAGGATGTAGTTACTCCTAACGTGGTTCGTAGCCAAGTGCCAGCTCTAACCACGACCTAT
GATATATCATCTCGATATATTATTGTCCAGGTGCCACCTTATATGAATTCTCCTCCACCATGTGCTCCCCAGTCTCAAAA
TGGTAATCCATCTGCAAGTGAATTTGCTTTTCACCATTATAACCCTAACTTTTTACCTCAGTTCACTGAAAATCAAGAAA
CCTTGAGCCCTCAGTTTACACAAACAGATGCAATGGATCATAGAAGATGGCCTGCATGGAAAGGACTGCCACCTTGTCCA
CCAACGTGGAGTCCACCTCCTTCAACCCTACGTGGTGGATCACATCATTCATACCAGAGAAGACATAGACCATATTAA

Alignment

ORF - retro_pabe_112 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.01 %
• Parental protein coverage: 73.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KAPPGDEEGFDYNEEERYDCKGGELFGNQRRFPGHLFWDFQINILGEKDDTPVHFCDKCGLPIKIYGRMI
          K.P.G..E...YN.E..Y..KG..L.......PG....D..INI.GEKDD.P.HFCDKC.LPIKIYGR.I
Retrocopy KMPAGKQE-CEYNKEGKYYSKGVKLVRKKKKIPGYHWGDIKINIIGEKDDSPIHFCDKCDLPIKIYGRII

Parental  PCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRA
          PCKH.FCYDCA.L..K.G.K.CP.C..PV.RIE...RGS.FMCS.V..CKRTYLSQ..LQAHI..RH.RA
Retrocopy PCKHAFCYDCANLDDKIGYKICPRCRYPVLRIEEHKRGSVFMCSVVPQCKRTYLSQKSLQAHIKRRHKRA

Parental  GKPVTRASLENVHPPIAPPPTEIPERFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRAP
          .K.VT.ASLE.V.P.IAPP.TEI.E......D..H.S.IPP.QH.MM..P..QH..HE..NQPH..I.AP
Retrocopy RKQVTSASLEKVRPHIAPPRTEISEIPKRLLDRDHLSYIPPEQHTMMSLPSVQHMLHEQHNQPHKAIQAP

Parental  PAELSMAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQP--VVSHP
          P.ELS..PP.P.....ET..I.TRKH.NL....IQ..S.SG...P.PP...P..........P.......
Retrocopy PPELSLSPPFP--IQWETVSIFTRKHGNLTVDHIQNNSDSGVKKPTPPDHHPEYQRQPAVSSPHHIIPQK

Parental  HHIMPPQQHYAPPPPPPP
          ....PP.....P...P.P
Retrocopy QRYAPPPSPSLPVNHPMP

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	12.16 RPM
SRP007412_cerebellum	0.00 RPM	10.46 RPM
SRP007412_heart	0.00 RPM	3.70 RPM
SRP007412_kidney	0.00 RPM	4.21 RPM
SRP007412_liver	0.00 RPM	3.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_112 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_112 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_49
Pan troglodytes	retro_ptro_67
Gorilla gorilla	retro_ggor_164
Canis familiaris	retro_cfam_2047

---

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,