RetrogeneDB ID: retro_pabe_3132

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:40135326..40136315(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000017602
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUBG1
• Ensembl ID: ENSPPYG00000008384
• Aliases: None
• Description: tubulin gamma-1 chain [Source:RefSeq peptide;Acc:NP_001125599]

Sequence

>retro_pabe_3132
ATGCCAAGAGAAAACATCACCCACAATTGGGCCAGTGCAGCAATCAGATTGGGTTCGAGTTCTGGAAACAGCTGTGCACT
GAGCATGGTATCAGCCCCAAGGGCATCATGGAGGAGTTCACCACTGAGGGCACTGACCGCAAGGACATCTTTTTCTACCA
GGCAGATGATGAGCACTACATCCCCTGGGCCGTGCTGCTAGACCTGGAGCCCTGGGTGATCCACTCCATCCTCAACTCCC
CCTGTGCCAAGCTCTACAACCCAGAGAACATCTACCTGTCGGAGCATGGAGGAAGAGCTGGCAACAACTGGGCCAGCAGA
TTCTCCCAGAGAGAGAAGATCCATGAGGACATTTTTAACATCACAGACCGGAAGGCAGATGGTAGTGACAATCTAGATGG
CTTTGTGCTGTGTCAGTCCATTGCTGGGGGGACAGGCTGTGGCCTGGGCTCCTACCTCTTAGAATGGCTGAATGACAGGT
ATCCTAAGAAGCTGGTGCAGACATACTCAGTGTTTCCCAACCAGGACAAGATGAGCAATATGGTGGTCCAGCTTTATAAT
TCACTCGTCACACTCAAGGGGCTGATGCAGAACGCAGACTGTGTGGTGGTACTGCACAACACACCCCTAAACCGGATTGC
CACAGACTGCCTGCACATCCAGAACCCACCCTTCTCTCAGACCAACCAGCTGGTGTCCACCATCATCTCGGCCACCACCA
TCACCCTGTGCTACCCCAGCTACATGAACAATGACCTCACTGGCTTCATCGCCTCACTCATTCCCACCCCATGGCTCCAC
TTTCTCATGACTGGCTACACCCCGCTGACTATGGACCAATCAGTGGCCAGCGTGAGGAAGACCATGGTCCTGGATGTCAT
GAGGTGGCTGCTGCAGCCCAAGGACGTGATGGTGTCCACAGGCCAAGACCACCAGACCAACCACTCCTACATCACCATCC
TCAACACCATCCAGGGTGGACCCCACCCA

Alignment

ORF - retro_pabe_3132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 73.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREIITL-QLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDL
          MPRE.IT..QLGQC.NQIGFEFWKQLC.EHGISP.GI.EEF.TEGTDRKD.FFYQADDEHYIP.AVLLDL
Retrocopy MPRENITH<QLGQCSNQIGFEFWKQLCTEHGISPKGIMEEFTTEGTDRKDIFFYQADDEHYIPWAVLLDL

Parental  EPRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCH
          EP.VIHSILNSP.AKLYNPENIYLSEHGG.AGNNWAS.FSQ.EKIHEDIF.I.DR.ADGSD.L.GFVLC.
Retrocopy EPWVIHSILNSPCAKLYNPENIYLSEHGGRAGNNWASRFSQREKIHEDIFNITDRKADGSDNLDGFVLCQ

Parental  SIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPYQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTA
          SIAGGTG.GLGSYLLE.LNDRYPKKLVQTYSVFP.QD.MS..VVQ.YNSL.TLK.L.QNADCVVVL.NT.
Retrocopy SIAGGTGCGLGSYLLEWLNDRYPKKLVQTYSVFPNQDKMSNMVVQLYNSLVTLKGLMQNADCVVVLHNTP

Parental  LNRIATDRLHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTD
          LNRIATD.LHIQNP.FSQ.NQLVSTI.SA.T.TL.YP.YMNNDL.G.IASLIPTP.LHFLMTGYTPLT.D
Retrocopy LNRIATDCLHIQNPPFSQTNQLVSTIISATTITLCYPSYMNNDLTGFIASLIPTPWLHFLMTGYTPLTMD

Parental  QSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDP
          QSVASVRKT.VLDVMR.LLQPK.VMVSTG.D.QTNH.YI.ILN.IQG...P
Retrocopy QSVASVRKTMVLDVMRWLLQPKDVMVSTGQDHQTNHSYITILNTIQGGPHP

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	0.33 RPM	73.70 RPM
SRP007412_cerebellum	0.36 RPM	41.10 RPM
SRP007412_heart	0.27 RPM	5.39 RPM
SRP007412_kidney	0.53 RPM	15.55 RPM
SRP007412_liver	0.09 RPM	4.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3132 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3132 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3725
Gorilla gorilla	retro_ggor_2515
Macaca mulatta	retro_mmul_1692

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004907	1 retrocopy	retro_cjac_4142,
Echinops telfairi	ENSETEG00000008542	1 retrocopy	retro_etel_496,
Homo sapiens	ENSG00000131462	1 retrocopy	retro_hsap_3725,
Gorilla gorilla	ENSGGOG00000010899	1 retrocopy	retro_ggor_2515,
Nomascus leucogenys	ENSNLEG00000011686	1 retrocopy	retro_nleu_71,
Pongo abelii	ENSPPYG00000008384	1 retrocopy	retro_pabe_3132 ,
Pan troglodytes	ENSPTRG00000009211	1 retrocopy	retro_ptro_2520,
Rattus norvegicus	ENSRNOG00000020213	2 retrocopies	retro_rnor_2070, retro_rnor_2072,
Tupaia belangeri	ENSTBEG00000015835	3 retrocopies	retro_tbel_188, retro_tbel_3516, retro_tbel_955,