RetrogeneDB ID: retro_ptro_2287

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:111405066..111407518(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCLAF1
• Ensembl ID: ENSPTRG00000018635
• Aliases: None
• Description: BCL2-associated transcription factor 1 [Source:HGNC Symbol;Acc:16863]

Sequence

>retro_ptro_2287
GGTCGCTCCAATTCTAGATCACATTCTTCAAGGTCAAAGTCTAGATGACAGTCTAGTTCTCGATCAAGATCAAGATCTCA
TTCTAGAAAGAAGCGATACAGTTCTAGGTCTTGTTCCAGAACATATTCAAGGTCTTGGAGTAGAGATCGTATGTATTCTA
GAGATGATCGTCGTGAGTACAGAAATAATAGAGGAATGAAGCGACCTTATGGGTACAGAGGAAGGGGTAGAGGGTATTAT
CAAGGAGGAGGAGGTAGATATCATCTAGGTGGTTATAGACCTGTCTGGAATAGAAGGCACTCTAGGAGTCCTAGACGAGG
TCGTTCACATTCCAGGAGTCCAAAAAGAAGATCCGTTTCTTCTCAAAGATCCAGAAGCAGATCTCACTGGTCATATAGCT
CTTCTAGGTCTCCAAGATCATTCTCTTCTCGTTCTTCATCTCCATATAGAAAATCTCCTGTTTCTAAAAGACAAGGGTCT
CAGGAAAAACAAGCCAAAAAAGCTGAAGGGGAACCCCAAGAAGAGAGTCCGTTGAAAACTAAATCACAGGAGGAACTGAA
AGATACATTTGAACATGATCCATCTGAGTCTATCGATGAATTTAGTAAGTCATCAGCCACATCCGGTGATATTTGGCCTG
GCCTTACAGCTTATAATAATAGTCCTAGATCACCCCATAGTCCTTCACCTATTGCTACACCACCTAGTCAGAGTTCATCT
TGCTCTGATGCTCCCATGCTCAGTACAGTTCACTCTGCAAAAAATACTCCTTCTCAGCATTCAAAATCCATTCAGCATAG
TCCTGAAAGGTCTGGGTCTGGTTCTGTTGGAAATGGATCTAGTCCATACAGTCCTTCTCAGAATAGTCCAGTTCATCACA
TCCCTTCACGAAGAAGTCCTGCAAAGACAATCGCACCACAGAATGCTCCAAGAGATGAGTCTAGGGGCCGTTCCTCATTT
TATCCTGATAATGGAGATCAGGAAACTGCAAAGACTGGGAAGTTCTTAAAAAGGTTCATAGATGAAGAGTCTAGAGTATT
CCTGCTTGATAGGGGTAATGCCAGGGATAAAGAGGCTTCAAAAGAGAAAGGATCAGAGAAAGGGAGGGCAGAGGGAGAAT
GGGAAGATCAGGAAGCTCTAGATTACTTCAGTGATAAAGAGTCTGGAAAACAAAGTTTAATGATTCAGAAGGGGATGGCA
CAGAGGAGACAGAGGATTATAGACAGCTCAGGAAGTCAGTCCTCACAGATCAAGGTAAAAGTTTTGCTACTGCATCTCAC
CGGAATACTGAGGAGGAAGGACTCAAGTAGAAGTCCAAAGTTTCACTGAAAGGCAATAGAGAAAGTGGTGGATTTAGAGA
AGGAAAAAATTATGAACTTAAAGAAGCTGGATATGTAGTGGAAAGGCCTAGCACTACAAAAGATAAGCACAAAGAGGAAG
ACAAAAATTCTGAAAGAATAACAGTAAAGAAAGAAACTCAGTCACCTGAGCAGGTAAAGTCTGAAAAGCTCAAAGACCTC
TTTGATTACAATCCGCCTCTACACAAGAATCTGGATGCATGAGAAAGTCTACCTTCAGAGAGGAAAGCCCACTTAGGATC
AAAATGATAGCAAGTGATTCTCATCGTCCTGAAGTCAAACTCAAAATGGCACCTGTTCCTCTTGATGATTCTAACAGACC
TGCTTCCTTGACTAAAGACAGGCGGCTTGCTAGTACACTTGTCCATTCTGTCAAGAAGGAGCAAGAATTCTCATCCATCT
TTGACCACATTAAGTTGCCACAGGCCAGCAAAAGCACTTCAGAGTCATTTATTTAACACATTGTGTTCTTGGTTCATCAT
GTTAAAGAGCAATACTTCAGGTCAGCTGCAATGACCCTAAACAAGCGGTTTACTTCCCATCAGGAAGCCACTGAAGAACA
TAGTACTCGGCAAAAGAGCCCTGAAATACACAGGAGAATTGACATCTCACCAAGTACCCTGAGGAAGCATACCCATTTAG
CAGGGGACGAGAGAGTTTTTAAAGAAGAAAATCAAAAGGGAGATAAAAAAAAATTAAGGTGTGACTCTGCTGACCTTCAG
CATGACATTGATCGCCGTAGAAAAGAAAGAAGTAAAGAACGGGGAAATTCCAAGGGCCCCAGGGAAACCAGTGGATCAAG
AAAGCAGGAAAAAACTCCAAAAGATTACAAGGAATACAAATCTTACAAAGATGACAGTAAACATAAAAATAGAGAGCAAG
ATCATTCTCGATCTTCATCCTCTTCACCATCACCTTCTTCTCCCAGTTCTAGAGAAGAAAAGGCGAGTAAGAAGGAAAGA
GAAGAAGAATTTAAAACTCACCATGAAATGAAAGAATACTCAGGCTTTGCAGGAGTTAGCCAACCATGAGGAACCTTTTT
TCGAATTAGAGGCAGAGGAAGAGACAGAGGAGTTTTTGCTGGGACAAATACT

Alignment

ORF - retro_ptro_2287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.44 %
• Parental protein coverage: 88.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GRSNSRSHSSRSKSRSQSSSRSRSRSHSRKKRYSSRSRSRTYSRSRSRDRMYSRDYRRDYRNNRGMRRPY
          GRSNSRSHSSRSKSR.QSSSRSRSRSHSRKKRYSSRS.SRTYSRS.SRDRMYSRD.RR.YRNNRGM.RPY
Retrocopy GRSNSRSHSSRSKSR*QSSSRSRSRSHSRKKRYSSRSCSRTYSRSWSRDRMYSRDDRREYRNNRGMKRPY

Parental  GYRGRGRGYYQGGGGRYHRGGYRPVWNRRHSRSPRRGRSRSRSPKRRSVSSQRSRSRSRRSYRSSRSPRS
          GYRGRGRGYYQGGGGRYH.GGYRPVWNRRHSRSPRRGRS.SRSPKRRSVSSQRSRSRS..SY.SSRSPRS
Retrocopy GYRGRGRGYYQGGGGRYHLGGYRPVWNRRHSRSPRRGRSHSRSPKRRSVSSQRSRSRSHWSYSSSRSPRS

Parental  SSSRSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDEFNKSSATSGD
          .SSRSSSPY.KSPVSKR.GSQEKQ.KKAEGEPQEESPLK.KSQEE.KDTFEHDPSESIDEF.KSSATSGD
Retrocopy FSSRSSSPYRKSPVSKRQGSQEKQAKKAEGEPQEESPLKTKSQEELKDTFEHDPSESIDEFSKSSATSGD

Parental  IWPGLSAYDNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGS
          IWPGL.AY.NSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHS.SIQHSPERSGSGSVGNGS
Retrocopy IWPGLTAYNNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSKSIQHSPERSGSGSVGNGS

Parental  SRYSPSQNSPIHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDGGDQETAKTGKFLKRFTDEESRVFLLD
          S.YSPSQNSP.HHIPSRRSPAKTIAPQNAPRDESRGRSSFYPD.GDQETAKTGKFLKRF.DEESRVFLLD
Retrocopy SPYSPSQNSPVHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDNGDQETAKTGKFLKRFIDEESRVFLLD

Parental  RGNTRDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ-KFNDSEGDDTEETEDYRQFRKSVLADQG
          RGN.RDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ.KFNDSEGD.TEETEDYRQ.RKSVL.DQG
Retrocopy RGNARDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ<KFNDSEGDGTEETEDYRQLRKSVLTDQG

Parental  KSFATASHRNTEEEGLKYKSKVSLKGSRESDGFREEKNYKLKETGYVVERPSTTKDKHKEEDKNSERITV
          KSFATASHRNTEEEGLK.KSKVSLKG.RES.GFRE.KNY.LKE.GYVVERPSTTKDKHKEEDKNSERITV
Retrocopy KSFATASHRNTEEEGLK*KSKVSLKGNRESGGFREGKNYELKEAGYVVERPSTTKDKHKEEDKNSERITV

Parental  KKETQSPEQVKSEKLKDLFDYSPPLHKNLDARE-KSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDDS
          KKETQSPEQVKSEKLKDLFDY.PPLHKNLDA.E.KSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDDS
Retrocopy KKETQSPEQVKSEKLKDLFDYNPPLHKNLDA*E<KSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDDS

Parental  NRPASLTKDRLLASTLVHSVKKEQEFRSIFDHIKLPQASKSTSESFIQHIVSLVHHVKEQYFKSAAMTLN
          NRPASLTKDR.LASTLVHSVKKEQEF.SIFDHIKLPQASKSTSESFI.HIV.LVHHVKEQYF.SAAMTLN
Retrocopy NRPASLTKDRRLASTLVHSVKKEQEFSSIFDHIKLPQASKSTSESFI*HIVFLVHHVKEQYFRSAAMTLN

Parental  ERFTSYQKATEEHSTRQKSPEIHRRIDISPSTLRKHTRLAGEERVFKEENQKGD-KKLRCDSADLRHDID
          .RFTS.Q.ATEEHSTRQKSPEIHRRIDISPSTLRKHT.LAG.ERVFKEENQKGD...LRCDSADL.HDID
Retrocopy KRFTSHQEATEEHSTRQKSPEIHRRIDISPSTLRKHTHLAGDERVFKEENQKGDXXXLRCDSADLQHDID

Parental  RRRKERSKERGDSKGSRESSGSRKQEKTPKDYKEYKSYKDDSKHK-REQDHSRSSSSSASPSSPSSREEK
          RRRKERSKERG.SKG.RE.SGSRKQEKTPKDYKEYKSYKDDSKHK.REQDHSRSSSSS.SPSSPSSREEK
Retrocopy RRRKERSKERGNSKGPRETSGSRKQEKTPKDYKEYKSYKDDSKHKNREQDHSRSSSSSPSPSSPSSREEK

Parental  ESKKEREEEFKTHHEMKEYSGFAGVSRPRGTFFRIRGRGRARGVFAGTNT
          .SKKEREEEFKTHHEMKEYSGFAGVS.P.GTFFRIRGRGR.RGVFAGTNT
Retrocopy ASKKEREEEFKTHHEMKEYSGFAGVSQP*GTFFRIRGRGRDRGVFAGTNT

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	0.02 RPM	75.86 RPM
SRP007412_cerebellum	0.14 RPM	148.02 RPM
SRP007412_heart	0.17 RPM	77.94 RPM
SRP007412_kidney	0.00 RPM	60.15 RPM
SRP007412_liver	0.03 RPM	41.47 RPM
SRP007412_testis	0.42 RPM	115.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2287 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2287 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3364
Pongo abelii	retro_pabe_2767
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	ENSPPYG00000017032	1 retrocopy	retro_pabe_2767,
Pan troglodytes	ENSPTRG00000000535	1 retrocopy	retro_ptro_1771,
Pan troglodytes	ENSPTRG00000018635	1 retrocopy	retro_ptro_2287 ,
Tupaia belangeri	ENSTBEG00000014886	1 retrocopy	retro_tbel_628,