RetrogeneDB ID: retro_hsap_3364

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:110284188..110286477(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000248966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BCLAF1
• Ensembl ID: ENSG00000029363
• Aliases: BCLAF1, BTF, bK211L9.1
• Description: BCL2-associated transcription factor 1 [Source:HGNC Symbol;Acc:16863]

Sequence

>retro_hsap_3364
GGTCGCTCCAATTCTAGATCACATTCTTCAAGGTCAAAGTCTAGATGACAGTCTAGTTCTCGATCAAGATCAAGATCTCA
TTCTAGAAAGAAGCGACACAGTTCTAGGTCTCGTTCCAGAACATATTCAAGGTCTTGGAGTAGAGATCGTATGTATTCTA
GAGATGATCGTCGTGAGTACAGAAATAATAGAGGAATGAAATGACCTTATGGGTACAGAGGAAGGGGTAGAGGGTATTAT
CAAGGAGGAGGAGGTAGATATCATCTAGGTGGTTATAGACCTGTCCGGAATAGGAGGCACTCTAGGAGTCCTAGACGAGG
TCGTTCACATTCCAGGAGTCCAAAAAGAAGATCCGTTTCTTCTCAAAGATCCAGAAGCAGATCTCACTGGTCATATAGCT
CTTCTAGGTCTCCAAGATCATTCTCTTCTCGTTCTTCATCTCCATATAGCAAATCTCCTGTTTCTAAAAGACGAGGGTCT
CAGGAAAAACAAGCCAAAAAAGCTGAAGGGGAACCCCAAGAAGAGAGTCCGTTGAAAACTAAATCACAGGAGGAACTGAA
AGATACATTTGAACATGATCCATCTGAGTCTATCGATGAATTTAGTAACTCATCAGCCACATCCGGTGATATTTGGCCTG
GCCTTACAGCTTATAATAATAGTCCCAGATCACCCCATAGTCCTTCACATATTGCTACACCACCTAGTCAGAGTTCATCT
TGCTCTGATGCTCCCATGCTCAGTACAGTTCACTCTGCAAAAAATACTCCTTCTCAGCATTCAAAATCCATTCAGCATAG
TCCTGAAAGGTCTGGGTCTGGTTCTGTTGGAAATGGATCTAGTCCATACAGTCCTTCTCAGAATAGTCCAGTTCATCACA
TCCCTTCACGAAGAAGTCCTGCAAAGACAATCGCACCACAGAATGCTCCAAGAGATGAGTCTAGGGGCCGTTCCTCATTT
TATCCTGATAATGGAGATCAGGAAACTGCAAAGACTGGGAAGTTCTAAAAAGGTTCACAGATGAAGAGTCTAGAGTATTC
CTGCTTGATAGGGGTAATGCCAGGGATAAAGAGGCTTCAAAAGAGAAAGGATCAGAGAAAGGGAGGGCAGAGGGAGAATG
GGAAGATCAGGAAGCTCTAGATTACTTCAGTGATAAAGAGTCTGGAAAACAAAGTTTAATGATTCAGAAGGGGATGGCAC
AGAGGAGACAGAGGATTATAGACAGTTCAGGAAGTCAGTCCTCACAGATCAAGGTAAAAGTTTTGCTGCTGCATCTCACC
GGAATACTGAGGAGGAAGGACTCAAGTACAAGTCCAAAGTTTCACTGAAAGGCAATAGAGAAAGTGGTGGATTTAGAGAA
GAAAAAAATTATGAACTTAAAGAAGCTGGATATGTAGTGGAAAGGCCTAGCACTACAAAAGATAAGCACAAAGAAGAAGA
CAAAAATTCTGAAAGAATAATAGTAAAGAAAGAAACTCAGTCACCTGAGCAGGTAAAGTCTGAAAAGCTCAAAGACCTCT
TTGATTACAATCCCCCTCTACACAAGAATCTGGATGCATGAGAAAGTCTACCTTCAGAGAGGAAAGCCCACTTAGGATCA
AAATGATAGCAAGTGATTCTCATCATCCTGAAGTCAAACTCAAAATGGCACCTGTTCCTCTTGATGATTCTAACAGACCT
GCTTCCTTGACTAAAGACAGGCGGCTTGCTAGTACACTTGTCCATTCTGTCAAGAAGGAGCAAGAATTCTGATCCATCTT
TGACCACATTAAGTTGCCACAGGCCAGCAAAAGCACTTCAGAGTCATTTATTTAACACATTGTGTTCTTGGTTCATCATG
TTAAAGAGCAATACTTCAGGTCAGCTGCAATGACCCTAAACAAGCGGTTTACTTCCCATCAGAAAGCCACTGAAGAACAT
AGTACTCGGCAAAAGAGCCCTGAAATACACAGGAGAATTGACATCTCACCAAGTACCCTGAGGAAGCATACCCATTTAGC
AGGGGACGAGAGAGTTTTTAAAGAAGAAAATCAAAAGGGAGATAAAAAAAAATTAAGGTGTGACTCTGCTGACCTTCAGC
ATGACATTGATCACCGTAGAAAAGAAATAAGTAAAGAACGGGGAAATTCCAAGGGCCCCAGGGAATCCAGTGGATCAAGA
AAGCAGGAAAAAACTCCAAAAGATTACAAGGAATACAAATCTTACAAAGATGACAGTAAACATAAAAATAGAGAGCAAGA
TCATTCTCGATCTTCATCCTCTTCACCATCACCTTCTTCTCCCAGTTCT

Alignment

ORF - retro_hsap_3364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 87.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRSNSRSHSSRSKSRSQSSSRSRSRSHSRKKRYSSRSRSRTYSRSRSRDRMYSRDYRRDYRNNRGMRRPY
          GRSNSRSHSSRSKSR.QSSSRSRSRSHSRKKR.SSRSRSRTYSRS.SRDRMYSRD.RR.YRNNRGM..PY
Retrocopy GRSNSRSHSSRSKSR*QSSSRSRSRSHSRKKRHSSRSRSRTYSRSWSRDRMYSRDDRREYRNNRGMK*PY

Parental  GYRGRGRGYYQGGGGRYHRGGYRPVWNRRHSRSPRRGRSRSRSPKRRSVSSQRSRSRSRRSYRSSRSPRS
          GYRGRGRGYYQGGGGRYH.GGYRPV.NRRHSRSPRRGRS.SRSPKRRSVSSQRSRSRS..SY.SSRSPRS
Retrocopy GYRGRGRGYYQGGGGRYHLGGYRPVRNRRHSRSPRRGRSHSRSPKRRSVSSQRSRSRSHWSYSSSRSPRS

Parental  SSSRSSSPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKSKSQEEPKDTFEHDPSESIDEFNKSSATSGD
          .SSRSSSPYSKSPVSKRRGSQEKQ.KKAEGEPQEESPLK.KSQEE.KDTFEHDPSESIDEF..SSATSGD
Retrocopy FSSRSSSPYSKSPVSKRRGSQEKQAKKAEGEPQEESPLKTKSQEELKDTFEHDPSESIDEFSNSSATSGD

Parental  IWPGLSAYDNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGS
          IWPGL.AY.NSPRSPHSPS.IATPPSQSSSCSDAPMLSTVHSAKNTPSQHS.SIQHSPERSGSGSVGNGS
Retrocopy IWPGLTAYNNSPRSPHSPSHIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSKSIQHSPERSGSGSVGNGS

Parental  SRYSPSQNSPIHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDGGDQETAKTGKF-LKRFTDEESRVFLL
          S.YSPSQNSP.HHIPSRRSPAKTIAPQNAPRDESRGRSSFYPD.GDQETAKTGKF.LKRFTDEESRVFLL
Retrocopy SPYSPSQNSPVHHIPSRRSPAKTIAPQNAPRDESRGRSSFYPDNGDQETAKTGKF<LKRFTDEESRVFLL

Parental  DRGNTRDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ-KFNDSEGDDTEETEDYRQFRKSVLADQ
          DRGN.RDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ.KFNDSEGD.TEETEDYRQFRKSVL.DQ
Retrocopy DRGNARDKEASKEKGSEKGRAEGEWEDQEALDYFSDKESGKQ<KFNDSEGDGTEETEDYRQFRKSVLTDQ

Parental  GKSFATASHRNTEEEGLKYKSKVSLKGNRESDGFREEKNYKLKETGYVVERPSTTKDKHKEEDKNSERIT
          GKSFA.ASHRNTEEEGLKYKSKVSLKGNRES.GFREEKNY.LKE.GYVVERPSTTKDKHKEEDKNSERI.
Retrocopy GKSFAAASHRNTEEEGLKYKSKVSLKGNRESGGFREEKNYELKEAGYVVERPSTTKDKHKEEDKNSERII

Parental  VKKETQSPEQVKSEKLKDLFDYSPPLHKNLDARE-KSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDD
          VKKETQSPEQVKSEKLKDLFDY.PPLHKNLDA.E.KSTFREESPLRIKMIASDSH.PEVKLKMAPVPLDD
Retrocopy VKKETQSPEQVKSEKLKDLFDYNPPLHKNLDA*E<KSTFREESPLRIKMIASDSHHPEVKLKMAPVPLDD

Parental  SNRPASLTKDRLLASTLVHSVKKEQEFRSIFDHIKLPQASKSTSESFIQHIVSLVHHVKEQYFKSAAMTL
          SNRPASLTKDR.LASTLVHSVKKEQEF.SIFDHIKLPQASKSTSESFI.HIV.LVHHVKEQYF.SAAMTL
Retrocopy SNRPASLTKDRRLASTLVHSVKKEQEF*SIFDHIKLPQASKSTSESFI*HIVFLVHHVKEQYFRSAAMTL

Parental  NERFTSYQKATEEHSTRQKSPEIHRRIDISPSTLRKHTRLAGEERVFKEENQKGD-KKLRCDSADLRHDI
          N.RFTS.QKATEEHSTRQKSPEIHRRIDISPSTLRKHT.LAG.ERVFKEENQKGD...LRCDSADL.HDI
Retrocopy NKRFTSHQKATEEHSTRQKSPEIHRRIDISPSTLRKHTHLAGDERVFKEENQKGDXXXLRCDSADLQHDI

Parental  DRRRKERSKERGDSKGSRESSGSRKQEKTPKDYKEYKSYKDDSKHK-REQDHSRSSSSSASPSSPSS
          D.RRKE.SKERG.SKG.RESSGSRKQEKTPKDYKEYKSYKDDSKHK.REQDHSRSSSSS.SPSSPSS
Retrocopy DHRRKEISKERGNSKGPRESSGSRKQEKTPKDYKEYKSYKDDSKHKNREQDHSRSSSSSPSPSSPSS

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
bodymap2_adipose	0.00 RPM	124.91 RPM
bodymap2_adrenal	0.02 RPM	198.55 RPM
bodymap2_brain	0.02 RPM	247.27 RPM
bodymap2_breast	0.02 RPM	128.46 RPM
bodymap2_colon	0.00 RPM	124.21 RPM
bodymap2_heart	0.02 RPM	104.29 RPM
bodymap2_kidney	0.00 RPM	164.64 RPM
bodymap2_liver	0.04 RPM	51.90 RPM
bodymap2_lung	0.00 RPM	112.15 RPM
bodymap2_lymph_node	0.00 RPM	187.41 RPM
bodymap2_ovary	0.02 RPM	288.11 RPM
bodymap2_prostate	0.00 RPM	208.05 RPM
bodymap2_skeletal_muscle	0.05 RPM	76.86 RPM
bodymap2_testis	0.08 RPM	227.05 RPM
bodymap2_thyroid	0.00 RPM	303.26 RPM
bodymap2_white_blood_cells	0.00 RPM	217.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3364 was not detected

EST

No EST(s) were mapped for retro_hsap_3364 retrocopy.

TSS

No TSS is located nearby retro_hsap_3364 retrocopy 5' end.

Lab

retro_hsap_3364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3364 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2287
Pongo abelii	retro_pabe_2767
Macaca mulatta	retro_mmul_2102

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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	ENSPTRG00000018635	1 retrocopy	retro_ptro_2287,
Tupaia belangeri	ENSTBEG00000014886	1 retrocopy	retro_tbel_628,