RetrogeneDB ID: retro_ptro_2520

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:38258158..38259513(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBG1
• Ensembl ID: ENSPTRG00000009211
• Aliases: TUBG1, TUBG2
• Description: Tubulin gamma chain [Source:UniProtKB/TrEMBL;Acc:H2QD29]

Sequence

>retro_ptro_2520
ATGCCAAGAGAAATCATCACCCACAATTGGGCCAGTGCAGCAATCAGATTGGGTTCGAGTTCTGGAAACAGCTGTGCACT
GAGCATGGTATCAGCCCCAAGGGCACCATGGAGGAGTTCGCCACTGAGGGCACTGACCACAAGGACATCTTTTTCTACCA
GGCAGACAATGAGCACTACATCCCCCGGGCTGTGCTGCTGGACCTGGAGCCCCAGGTGATCCACTCCATCCTCAACTCCC
CCTGTGCCAAGCTCTACAACCCAGAGAACATCTACCTGTCGGAGCATGGAGGAAGAGCTGGCAACAACTGGGCCAGCAGA
TTCTCCCAGAGGGAGAAGATCCATGAGGACATTTTTAACATCACAGACCAGGAGGCAGATGGTAGTGACAATCTAGATGG
CTTTGTGCTGTGTCGGTTCATTGCTGGGGGGACAGGCTCTGGCCTGGGCTCCTACCTCTTACAATGGCTGAATGACAGGT
ATCCTAAGAAGCTGGTGCAGACATACTCAGTGTTTCCCAACCAGGACAAGATGAGCAACGTGGCGGTCCAGCTTTATAAT
TCACTCCTCACACTCAAGAGGCTGATGCAGAACGGAGACTGTGTGGTGGTGCTGCACAACACAGCCCTGAACCAGATTGC
CACAGACCAGATCCTGCACATCCAGAACCCATCCTTCTCTCAGACCAACCAGCTGGTGTCCACCATCATCTCGGCCAGCA
CCATCACCCTGCGCTACCCCAGCTACATGAACAATGACCTCATAGGCCTCATCGCCTCACTCATTCCCACCCCATGGCTC
CACTTTCTCATGACTGGCTACACCCCGCTGACTATGGACCAATCAGTGGCCAGCGTGAGGAAGACCATGGTCCTGGATGT
CATGAGGTGGCTGCTGCAGCCCAAGAACGTGATGGTATCCACAGGCCGAGACCGCCAGACCAACCACTCCTACATCACCA
TCCTCAACACCATCCAGGGAGAGGTGGACCCCACCCAGGTCCACAAGAGCCTGCAGAGGATCCGGGAACGGAAGTTGGCC
AACTTCATCCTGTTGGGCCCCACCAGCATCCAGGTGGCCCTGTCGAGGAAGTCTCCTTACCTGCCCTTGGCCCACCGGGT
CAGTGGGCTCATGATGGCCAACCACACCAGCATCTCCTCACTCTTCGAGAGAACCTGTCGCCAATATGACAAGCTGCGGA
AGTGGGAGGCCTTCCTGGAGCCGTTCCGCAAGGAGGACATGTTCAAGGACAACTTTGATGAGATGGACACATCTAGGGAG
ATTGTGCAGCAGCTCATGGATGAGTACCACATGGCCACATGGCCAGACTACATCTCCTGGGGCACCCAGGAGCAG

Alignment

ORF - retro_ptro_2520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREIITL-QLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDL
          MPREIIT..QLGQC.NQIGFEFWKQLC.EHGISP.G..EEFATEGTD.KD.FFYQAD.EHYIPRAVLLDL
Retrocopy MPREIITH<QLGQCSNQIGFEFWKQLCTEHGISPKGTMEEFATEGTDHKDIFFYQADNEHYIPRAVLLDL

Parental  EPRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCH
          EP.VIHSILNSP.AKLYNPENIYLSEHGG.AGNNWAS.FSQ.EKIHEDIF.I.D.EADGSD.L.GFVLC.
Retrocopy EPQVIHSILNSPCAKLYNPENIYLSEHGGRAGNNWASRFSQREKIHEDIFNITDQEADGSDNLDGFVLCR

Parental  SIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTA
          .IAGGTGSGLGSYLL..LNDRYPKKLVQTYSVFPNQD.MS.V.VQ.YNSLLTLKRL.QN.DCVVVL.NTA
Retrocopy FIAGGTGSGLGSYLLQWLNDRYPKKLVQTYSVFPNQDKMSNVAVQLYNSLLTLKRLMQNGDCVVVLHNTA

Parental  LNRIATDR-LHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTT
          LN.IATD..LHIQNPSFSQ.NQLVSTI.SAST.TLRYP.YMNNDLIGLIASLIPTP.LHFLMTGYTPLT.
Retrocopy LNQIATDQILHIQNPSFSQTNQLVSTIISASTITLRYPSYMNNDLIGLIASLIPTPWLHFLMTGYTPLTM

Parental  DQSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANF
          DQSVASVRKT.VLDVMR.LLQPKNVMVSTGRDRQTNH.YI.ILN.IQGEVDPTQVHKSLQRIRERKLANF
Retrocopy DQSVASVRKTMVLDVMRWLLQPKNVMVSTGRDRQTNHSYITILNTIQGEVDPTQVHKSLQRIRERKLANF

Parental  IPWGPASIQVALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNF
          I..GP.SIQVALSRKSPYLP.AHRVSGLMMANHTSISSLFERTCRQYDKLRK.EAFLE.FRKEDMFKDNF
Retrocopy ILLGPTSIQVALSRKSPYLPLAHRVSGLMMANHTSISSLFERTCRQYDKLRKWEAFLEPFRKEDMFKDNF

Parental  DEMDTSREIVQQLIDEYHAATRPDYISWGTQEQ
          DEMDTSREIVQQL.DEYH.AT.PDYISWGTQEQ
Retrocopy DEMDTSREIVQQLMDEYHMATWPDYISWGTQEQ

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	0.46 RPM	29.55 RPM
SRP007412_cerebellum	0.61 RPM	23.52 RPM
SRP007412_heart	0.09 RPM	24.80 RPM
SRP007412_kidney	0.55 RPM	51.39 RPM
SRP007412_liver	0.10 RPM	30.80 RPM
SRP007412_testis	0.42 RPM	243.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2520 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 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,
Macaca mulatta	ENSMMUG00000016797	1 retrocopy	retro_mmul_1692,
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,