RetrogeneDB ID: retro_pabe_2767

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:111760729..111762114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCLAF1
• Ensembl ID: ENSPPYG00000017032
• Aliases: None
• Description: BCL2-associated transcription factor 1 [Source:HGNC Symbol;Acc:16863]

Sequence

>retro_pabe_2767
ATGGGTCGCTCCAATTCTAGATCACGTTCTTCAAGGTCAAAGTCTAGATCACAGTCTAGTTCTCGATCAAGATCAAGATC
TCATTCTATAAAGAAGTGATACAGTTCTAGATCTTGTTCCAGAACATATTCAAGGTCTTGTAGTAGAGATCGTATGTATT
CTAGAGATGATCGTTGTGATTACAGAAATAATAGAGGAATGAAACGAGCGTATGGGTACAGAGGAAGGGGTAGAGGGTAT
TATCAAGGAGGAGGAGGTAGATATCATGGAGGTGGTTATAGACCTGTATGGAATAGAAGGCACTCTTGGAGTCCTAGATG
AGGTTGTTCACATTCCAGGAGTCCAAAAAGAAGATCCATTTCTTCTCAAAGATCCAGAAGCAGATCTCGCCGGTCATATA
GCTCTTCTAGGTCTCCAAGGTCATCCTCTTTTCGTTCTTCATCTCCATATAGCAAATCTCCTGTTTCTAAAAGACGAGGG
TCTCAGGAAAAACAAACCAAAAAAGCTGAAGGGGAACCCCAAGAAGAGAGTCCGTTGAAAAGTAAATCACAGGAGGAGCC
GAAAGATACATTTGAACATGATCCATCTGAGTCTATTGATGAAATTAATAAGTCATCAGCCACATCCCATGATATTTGGC
CTGGCCTTACAGCTTATGATAATAGTCCCTGATCACCCCATAGTCCTTCACCTAATGCTACACCACCTAATCAGAGTTCA
TCTTGCTCTGATGCTCCCATGCTCAGTACAGTTCACTCTGCAAAAAATACTCCTTCTCAGCATTCACAATCCATTCAGCA
TAGTCCTGAAAGGTCTGGGTCTGGTTCTGTTGGAAATGGATCTAGTCGATACAGTCCTTCTCAGAATAGTCCAATTCATC
ACGTTCCTTCACAAAGAAGTCCTGCAAAGACAATCGCACCACAGAATGCTCCAAGAAATGAGTCTAGGGGCCGTTCCTCA
TTTTATCCTGATGGTGGAGATCAGGAAACTGCAAAGACTGAGAAGTTCTTAAAAAGGTTCACAGATGAAGAGTCTAGATT
ATTCCTGCTTGATAGGGGTAATGCCACGGATAAAGAGGCTTCAAAATAGAAAGGATCAGAGAAAGGGAGGGTAGAGGGAG
AATGGGAAGATCAGGAAGCTCTAGATTACTTCAGTGATAAAGATTCTGGAAAACAAAAGTTTAATGATTCAGAAGGGGAT
GACACAGAGGAGACAGAGGATTATAGACAGTTCAGGAAGTCAGTCCTCGCAGATCAGGGTAAAAGTTTGCTACTGCATCT
CACCGGAATACTGAGGAGGAAGGACTCAAGTACAAGTCCAAAGTTTCACTGAAACGCAATAGAGAAAGTGGTGGATTTAG
AGAAGAAAAAAATTATAAACTTAGG

Alignment

ORF - retro_pabe_2767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGRSNSRSHSSRSKSRSQSSSRSRSRSHSRKKRYSSRSRSRTYSRSRSRDRMYSRDYRRDYRNNRGMRRP
          MGRSNSRS.SSRSKSRSQSSSRSRSRSHS.KK.YSSRS.SRTYSRS.SRDRMYSRD.R.DYRNNRGM.R.
Retrocopy MGRSNSRSRSSRSKSRSQSSSRSRSRSHSIKK*YSSRSCSRTYSRSCSRDRMYSRDDRCDYRNNRGMKRA

Parental  YGYRGRGRGYYQGGGGRYHRGGYRPVWNRRHSRSPRRGRSRSRSPKRRSVSSQRSRSRSRRSYRSSRSPR
          YGYRGRGRGYYQGGGGRYH.GGYRPVWNRRHS.SPR.G.S.SRSPKRRS.SSQRSRSRSRRSY.SSRSPR
Retrocopy YGYRGRGRGYYQGGGGRYHGGGYRPVWNRRHSWSPR*GCSHSRSPKRRSISSQRSRSRSRRSYSSSRSPR

Parental  SSSSRSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDEFNKSSATSG
          SSS.RSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDE.NKSSATS.
Retrocopy SSSFRSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDEINKSSATSH

Parental  DIWPGLSAYDNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNG
          DIWPGL.AYDNSP.SPHSPSP.ATPP.QSSSCSDAPMLSTVHSAKNTPSQHS.SIQHSPERSGSGSVGNG
Retrocopy DIWPGLTAYDNSP*SPHSPSPNATPPNQSSSCSDAPMLSTVHSAKNTPSQHSQSIQHSPERSGSGSVGNG

Parental  SSRYSPSQNSPIHHIPSRRSPAKTITPQNAPRDESRGRSSFYPDGGDQETAKTGKFLKRFTDEESRVFLL
          SSRYSPSQNSPIHH.PS.RSPAKTI.PQNAPR.ESRGRSSFYPDGGDQETAKT.KFLKRFTDEESR.FLL
Retrocopy SSRYSPSQNSPIHHVPSQRSPAKTIAPQNAPRNESRGRSSFYPDGGDQETAKTEKFLKRFTDEESRLFLL

Parental  DRGNTRDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQKFNDSEGDDTEETEDYRQFRKSVLADQG
          DRGN..DKEASK.KGSEKGR.EGEWEDQEALDYFSDK.SGKQKFNDSEGDDTEETEDYRQFRKSVLADQG
Retrocopy DRGNATDKEASK*KGSEKGRVEGEWEDQEALDYFSDKDSGKQKFNDSEGDDTEETEDYRQFRKSVLADQG

Parental  KS-FATASHRNTEEEGLKYKSKVSLKGNRESDGFREEKNYKLK
          KS.FATASHRNTEEEGLKYKSKVSLK.NRES.GFREEKNYKL.
Retrocopy KS<FATASHRNTEEEGLKYKSKVSLKRNRESGGFREEKNYKLR

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	78.57 RPM
SRP007412_cerebellum	0.00 RPM	145.68 RPM
SRP007412_heart	0.00 RPM	55.78 RPM
SRP007412_kidney	0.03 RPM	55.65 RPM
SRP007412_liver	0.00 RPM	50.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2767 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2767 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3364
Pan troglodytes	retro_ptro_2287
Macaca mulatta	retro_mmul_2102

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000027614	1 retrocopy	retro_fcat_978,
Homo sapiens	ENSG00000029363	1 retrocopy	retro_hsap_3364,
Gorilla gorilla	ENSGGOG00000001824	1 retrocopy	retro_ggor_2279,
Macaca mulatta	ENSMMUG00000003710	1 retrocopy	retro_mmul_2102,
Pongo abelii	ENSPPYG00000001544	1 retrocopy	retro_pabe_2336,
Pongo abelii	ENSPPYG00000017032	1 retrocopy	retro_pabe_2767 ,
Pan troglodytes	ENSPTRG00000018635	1 retrocopy	retro_ptro_2287,
Tupaia belangeri	ENSTBEG00000014886	1 retrocopy	retro_tbel_628,