RetrogeneDB ID: retro_tbel_628

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2595:105163..106561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCLAF1
• Ensembl ID: ENSTBEG00000014886
• Aliases: None
• Description: BCL2-associated transcription factor 1 [Source:HGNC Symbol;Acc:16863]

Sequence

>retro_tbel_628
TCCCCATATAGCAAATCCACTGTCTCTAAAAGATGAGGGTCTCAGGAAAAACAAACCAAAAAAGCTGAAGGGGAGCCCCA
AGAGGAGAGTCCTTTGAAAAATAAATCACAAGAAGAACCAAAAGATACATTTGAACATGACCCATCTGAATCAATTGATG
AGTTTAATAAATCATCGGCCATGTCTGGTGATATTTGGCCTGGCCTTTCAGCTTATGATAATAGTTCCAGATCACCCCAT
AGTCCTTCACCTATTGCTATACCACCTAGTCAGAGTTCATCTTGTTCTGATGCCCCCATGCTCAGTACAGTCCACTCTGC
AAAAAACACCCCCTCTCAGCATTCACATTCCATTCAGCATAGTCCTGAAAGGTCTGGGTCAGGGTCTGTTGGAAATGGAT
CTAGTAGGTATAGTCCTTCTCTGAATAGTCCAATTCATCACATCCCTTTATGAAGAAGTCCTGCAAAAGACAATCACACC
ACAGAATGCTCCAAGAGAGGAGTCTAGGGGACACTCTTCATTTTATCATGATGGTGGGGATCAGGAAACCACAAAGACTG
GAAAGTTCTTAAAAAGGTTCACAGATGAAGAGTCTAGAGTATTCCTGCTTGAGAGGAGAAGTACCAGGGATAAAGAGACT
CCAAAGGAAAAAGGATCAGAGAAAGGCAGGGCAGAAGGAGAATGGGAAGATCAGGAACCTCTAGATTACTTCAGTGATAA
AGAGTCCGGAAAACAAAAGTTTAATGATTCAGAAGGGGATGACACAGAGGAAACAGAGGATTATAGGCAGTTCAGAAAGT
CAGTCCTTGCAGATCAGGGTAAAAAGTTTGCTACTGCATCTGATCGGAATACTGAGGAGGAAGGACACAAGTACAAGTCT
AAAGTTTCACTGAAAGGCAGTTGGGAAAGTGATGGATTTAGAGAAGAAAAAATTATAAACTTAAAGAGACTGGATATGTA
GTGGAAAGGCCTAGCACTACAAAAGATAAGCACGAAGAAGACAAAAGTTCTGAAAGAATAACAGTAAAGAAAGAAACTCA
ATCACCTGAGCAGGTAAAGCCTGAAAAGCTCAAAGACCTCTTTGATTACGGTCCCCCTTTACACAAGAGTCTGGATGCAC
GGGAAAAATCTACCTTCAGAGAGGAGAGCCCACTTAGGATCAAAATGATAGCTCATCGTTCCGAAGTCAAACTCAAAATG
GCACCTGTTCCTCTTGATGATTCTAACAGACCTGCTTCCTTGACTAAAGACAGGCTACTTGCTAGTACACTTGTCCATTC
TGTCAAGAAGGAGCAAGAATTCCGATCCATCTTTGACCACATTAAGTTGCCACAGACCAGCAAAAGCACTTCAGAGTCAT
TTATTCAACACATTGTTTCCTTGGTTCATCATGTTAAA

Alignment

ORF - retro_tbel_628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 51.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPYSKSPVSKRRGSQEKQTKKAEGEPQEESPLKNKSQEEPKDTFEHDPSESIDEFNKSSATSGDIWPGLS
          SPYSKS.VSKR.GSQEKQTKKAEGEPQEESPLKNKSQEEPKDTFEHDPSESIDEFNKSSA.SGDIWPGLS
Retrocopy SPYSKSTVSKR*GSQEKQTKKAEGEPQEESPLKNKSQEEPKDTFEHDPSESIDEFNKSSAMSGDIWPGLS

Parental  AYDNSPRSPHSPSPIATPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGSSRYSPS
          AYDNS.RSPHSPSPIA.PPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGSSRYSPS
Retrocopy AYDNSSRSPHSPSPIAIPPSQSSSCSDAPMLSTVHSAKNTPSQHSHSIQHSPERSGSGSVGNGSSRYSPS

Parental  QNSPIHHIPSRRSPAK-TITPQNAPREESRGRSSFYPDGGDQETAKTGKFLKRFTDEESRVFLLERGNTR
          .NSPIHHIP..RSPAK.TITPQNAPREESRG.SSFY.DGGDQET.KTGKFLKRFTDEESRVFLLER..TR
Retrocopy LNSPIHHIPL*RSPAK>TITPQNAPREESRGHSSFYHDGGDQETTKTGKFLKRFTDEESRVFLLERRSTR

Parental  DKETPKEKGSEKGRAEGEWEDQEPLDYFSDKESGKQKFNDSEGDDTEETEDYRQFRKSVLADQGKNFATA
          DKETPKEKGSEKGRAEGEWEDQEPLDYFSDKESGKQKFNDSEGDDTEETEDYRQFRKSVLADQGK.FATA
Retrocopy DKETPKEKGSEKGRAEGEWEDQEPLDYFSDKESGKQKFNDSEGDDTEETEDYRQFRKSVLADQGKKFATA

Parental  SHRNTEEEGHKYKSKVSLKGSRESDGFREE-KNYKLKETGYVVERPSTTKDKHKEDDKSSERITVKKETQ
          S.RNTEEEGHKYKSKVSLKGS.ESDGFREE.KNYKLKETGYVVERPSTTKDKH.E.DKSSERITVKKETQ
Retrocopy SDRNTEEEGHKYKSKVSLKGSWESDGFREE<KNYKLKETGYVVERPSTTKDKH-EEDKSSERITVKKETQ

Parental  SPEQVKSEKLKDLFDYSPPLHKNLDAREKSTFREESPLRIKMIASDSHRPEVKLKMAPVPLDDSNRPASL
          SPEQVK.EKLKDLFDY.PPLHK.LDAREKSTFREESPLRIKMIA...HR.EVKLKMAPVPLDDSNRPASL
Retrocopy SPEQVKPEKLKDLFDYGPPLHKSLDAREKSTFREESPLRIKMIA---HRSEVKLKMAPVPLDDSNRPASL

Parental  TKDRLLASTLVHSVKKEQEFRSIFDHIKLPQASKSTSESFIQHIVSLVHHVK
          TKDRLLASTLVHSVKKEQEFRSIFDHIKLPQ.SKSTSESFIQHIVSLVHHVK
Retrocopy TKDRLLASTLVHSVKKEQEFRSIFDHIKLPQTSKSTSESFIQHIVSLVHHVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_628 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_628 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,