RetrogeneDB ID: retro_pabe_3250

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:30301552..30302879(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB1
• Ensembl ID: ENSPPYG00000011180
• Aliases: None
• Description: tubulin, beta 1 class VI [Source:HGNC Symbol;Acc:16257]

Sequence

>retro_pabe_3250
ATGAGGGAAATCGTGCACATCCAGGCTGGTCAGTGTGGCGACCAGATCGATGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCGACCCCACTGGCACCTACCACGGGGACAGCGACCTGCAGCTGGACTGCATCTCCGTGTATTACAATGAAG
CCACAGGTGGCAAATATGTTCCTCGTGCCATCCTGGTGGATCTAGAACCTGACACCGTGGACTCTGTTCGCTCAGGTCCT
TTTGGCCAGATCTTTAGACCAGACAACTTTGTATTTGGTCAGTCTGGGGCAGGTAACAACTGGGCCAAAGGCCACTACAC
AGAGGGCACTGAGCTGGTTGATTCTGTCCTGGATGTGGTACGGAAGGAGGCAGAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCACTGGGTGGGGGCACAGGCTCTGGAATGGGCACTCTCCTTATCAGCAAGATCCGAGAAGAATACCCT
GATCGCATCATGAATACCTTCAGTGTGGTGCCTTCACCCAAAGTGTCTGACACCGTGGTCGAGCCCTACAATGCTACCCT
CTCCGTCCATCACTTGGTAGAGAACACTGATGAGTTGCATTGACAACGAGGCCCTCTATGATATCTGCTTCCGCACTCTG
AAGCTGACCACACCAACCTATGGGGATCTGAACCACCTCGTCTCAGACACCATGAGCGGTGTCACCACCTGCCTCCGCTT
CCCTGGCCAGCTCAGTGCTGACCTCTGCAAGTTGGCAGTCAACATGGTCCCCTTCCCACGTCTCTATTTCTTTATGCCTG
GCTTTGCCCCTCTCACCAACCATGGAAGCCAACAGTATCGAGCTCTCACAGTGCCGGAACTCACCCAGCAGGTCTTCGAT
GCCAAGAACATGAGGGCTGCCTGTGACCCCCGCCACGGCCGATACCTCACCGTGGCTGCTGTCTTCCATGGTCGGATGTC
CATGAAGGAGGTCAATGAGCAGATGCGTAACGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAACAACG
TCAAGACAGCTGTCTGTTCCATCCCACCTCATGGCCTCAAGATGGCAGTCACCTTCATTGGGAATAGCACGGCCATCCAG
GAGCTCTTCAAGCACATCTCGGAGCAGTTCACTGCCATGTTCCGCCGGAAGGCCTTCCTCCACTCGTACACAGGCGAGGG
CATGGACGAGATGGAGTTCACCGAGGCTGAGAGCAACATGAACGACCTCGTCTCTGAGAATCAGCAGTACCAGGATGCCA
CCGCAGAAGCGGAGGAGGATTTCGGTGAGGAGGCCGAAGAGGAGGCC

Alignment

ORF - retro_pabe_3250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 97.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQIGQCGNQIGAKFWEMIGEEHGIDLAGSDCGASALQLERISVYYNEAYGRKYVPRAVLVDLEP
          MREIVHIQ.GQCG.QI.AKFWE.I..EHGID..G...G.S.LQL..ISVYYNEA.G.KYVPRA.LVDLEP
Retrocopy MREIVHIQAGQCGDQIDAKFWEVISDEHGIDPTGTYHGDSDLQLDCISVYYNEATGGKYVPRAILVDLEP

Parental  GTMDSIRSSKLGALFQPDSFVHGNSGAGNNWAKGHYTEGAELIENVLEVVRHESESCDCLQGFQIVHSLG
          .T.DS.RS...G..F.PD.FV.G.SGAGNNWAKGHYTEG.EL...VL.VVR.E.ESCDCLQGFQ..HSLG
Retrocopy DTVDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGTELVDSVLDVVRKEAESCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLMNKIREEYPDRIMNSFSVMPSPKVSDTVVEPYNAVLSIHQLIENAD-ACFCIDNEALYD
          GGTGSGMGTLL..KIREEYPDRIMN.FSV.PSPKVSDTVVEPYNA.LS.H.L.EN.D..C..IDNEALYD
Retrocopy GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHHLVENTD>SC--IDNEALYD

Parental  ICFRTLKLTTPTYGDLNHLVSLTMSGITTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAQGSQ
          ICFRTLKLTTPTYGDLNHLVS.TMSG.TT.LRFPGQL.ADL.KLAVNMVPFPRL.FFMPGFAPLT..GSQ
Retrocopy ICFRTLKLTTPTYGDLNHLVSDTMSGVTTCLRFPGQLSADLCKLAVNMVPFPRLYFFMPGFAPLTNHGSQ

Parental  QYRALSVAELTQQMFDARNTMAACDPRRGRYLTVACIFRGKMSTKEVDQQLLSVQTRNSSCFVEWIPNNV
          QYRAL.V.ELTQQ.FDA.N..AACDPR.GRYLTVA..F.G.MS.KEV..Q...VQ..NSS.FVEWIPNNV
Retrocopy QYRALTVPELTQQVFDAKNMRAACDPRHGRYLTVAAVFHGRMSMKEVNEQMRNVQNKNSSYFVEWIPNNV

Parental  KVAVCDIPPRGLSMAATFIGNNTAIQEIFNRVSEHFSAMFKRKAFVHWYTSEGMDINEFGEAESNIHDLV
          K.AVC.IPP.GL.MA.TFIGN.TAIQE.F...SE.F.AMF.RKAF.H.YT.EGMD..EF.EAESN..DLV
Retrocopy KTAVCSIPPHGLKMAVTFIGNSTAIQELFKHISEQFTAMFRRKAFLHSYTGEGMDEMEFTEAESNMNDLV

Parental  SEYQQFQDAKAVLEED--EEGMEEA
          SE.QQ.QDA.A..EED..EE..EEA
Retrocopy SENQQYQDATAEAEEDFGEEAEEEA

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	0.06 RPM	0.17 RPM
SRP007412_cerebellum	0.24 RPM	0.73 RPM
SRP007412_heart	0.06 RPM	0.36 RPM
SRP007412_kidney	0.17 RPM	0.53 RPM
SRP007412_liver	0.09 RPM	0.89 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3250 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3250 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3944
Pan troglodytes	retro_ptro_2677
Gorilla gorilla	retro_ggor_2651

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Dipodomys ordii	ENSDORG00000015889	1 retrocopy	retro_dord_254,
Homo sapiens	ENSG00000173213	1 retrocopy	retro_hsap_3733,
Homo sapiens	ENSG00000173876	1 retrocopy	retro_hsap_3944,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250 ,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,