RetrogeneDB ID: retro_ptro_2527

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:54284347..54285676(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSPTRG00000017939
• Aliases: TUBB, TUBB2A
• Description: Pan troglodytes tubulin, beta (TUBB), mRNA. [Source:RefSeq mRNA;Acc:NM_001045509]

Sequence

>retro_ptro_2527
ATGAAGGAAATTGTGCACATCCAAGCCAGTCACTGTGGCAACCAGATCGGTGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCAACCCACCGGCACCTACCACAGGGACAGTGCCCTGCAGCTGGACCGCATCTCCGTGTACTACAATGAAGC
CACAGGTGGCAAATATGTTCCTCATGCCATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGTTCACTCAGGTCCTT
TTGGCCAGATCTTTAGACCAGACAACTTTGCTTCTGATCAGTCTGGGGCAGGCAACAACTGGGCCAAAGGCCACTACACA
GAGGGGGCTGAGCTGGTTTATTCGGTCCTGGATTTGGTATGGAAGGAGGCGGAGAGCTGTGACTGCCTTCAGGGCTTCCA
GCTGACCCACTCACTTGACTGGGACACAGGCTCTGGAATCGGCACTCTCCTTATGAGCAAGATCCAAGAAGAGTACCCTG
ATTGCTTCATGAATACCTTCAGTGTGGTACCTTCACACAAGGTATCTGACACCGTGGTTGAGCCGTACAATGCCACCCTC
TCCGTCCATCAGTTGGTAGAGAACACTGATGAGACCTATTACATTGACAATGAGGCCCTCTAGGATATCTGCTTCCGCAA
TCTGAAGCTGACCACACCAACCTACTGGGATCTGAACTACCTCGTCTTAGCCACCATGAGTGGTGTCACCACCTGCCTCC
ACTTCCTGGCCAGCTCAGTGCTGACCTCTGCAAGTTGGCAGTCAACATGGTTCCCTTCCCATATCTCCATTTCTTTATGC
CTGGCTTTGCCCCTTTCACCAGCTGTGGAAGCCAGTAGTATCAAGCTCTCACTGTGCCCCAACTTACCCAGCGGGTCTTC
GATGCCAAAAACCTGATGGCTGCTTGTGACCCCCACCACGGCCAATACCTCACCATGGCTGCTGTCTCCAGTGGTCGGAT
GTCCATGAAGGAGGTCAATGAGCAGATGCTCAAAGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAACA
ACATCAAGACAGCTGTCTGTGACATCCACCTCATGGCCTCAAGATGGCTGTCACCTTCATCGGAAGCAGCACTGGCATCC
AGTAGCTCTTCAAGCGCATCTCGGAGCAGTTCACTGCCATGTTCTACCAGAAGGCCTTCCTCCACTGCTACACAGGCGAG
GGCATGGACGAGATGGAGTTCACTGAGGCTGAGAGCAACATGAACAACTTCGTCTCTGAGGATCAGCAGTACCAGGATGC
TACCACAGAAGAGGAAGAGGATTTCAGTAAGGAGGCTGAAGAGGAGGCC

Alignment

ORF - retro_ptro_2527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDP-TGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLE
          M.EIVHIQA..CGNQIGAKFWEVISDEHGI.P.TGTYH.DS.LQLDRISVYYNEATGGKYVP.AILVDLE
Retrocopy MKEIVHIQASHCGNQIGAKFWEVISDEHGINP<TGTYHRDSALQLDRISVYYNEATGGKYVPHAILVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          PGTMDSV.SGPFGQIFRPDNF...QSGAGNNWAKGHYTEGAELV.SVLD.V.KEAESCDCLQGFQLTHSL
Retrocopy PGTMDSVHSGPFGQIFRPDNFASDQSGAGNNWAKGHYTEGAELVYSVLDLVWKEAESCDCLQGFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYD
          ...TGSG.GTLL.SKI.EEYPD..MNTFSVVPS.KVSDTVVEPYNATLSVHQLVENTDETY.IDNEAL.D
Retrocopy DWDTGSGIGTLLMSKIQEEYPDCFMNTFSVVPSHKVSDTVVEPYNATLSVHQLVENTDETYYIDNEAL*D

Parental  ICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRF-PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          ICFR.LKLTTPTY.DLN.LV.ATMSGVTTCL.F.PGQL.ADL.KLAVNMVPFP.LHFFMPGFAP.TS.GS
Retrocopy ICFRNLKLTTPTYWDLNYLVLATMSGVTTCLHF<PGQLSADLCKLAVNMVPFPYLHFFMPGFAPFTSCGS

Parental  QQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNN
          Q.Y.ALTVP.LTQ.VFDAKN.MAACDP.HG.YLT.AAV..GRMSMKEV.EQML.VQNKNSSYFVEWIPNN
Retrocopy Q*YQALTVPQLTQRVFDAKNLMAACDPHHGQYLTMAAVSSGRMSMKEVNEQMLKVQNKNSSYFVEWIPNN

Parental  VKTAVCDI-PPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMND
          .KTAVCDI.PP.GLKMAVTFIG.ST.IQ.LFKRISEQFTAMF..KAFLH.YTGEGMDEMEFTEAESNMN.
Retrocopy IKTAVCDI<PPHGLKMAVTFIGSSTGIQ*LFKRISEQFTAMFYQKAFLHCYTGEGMDEMEFTEAESNMNN

Parental  LVSEYQQYQDATAEEEEDFGEEAEEEA
          .VSE.QQYQDAT.EEEEDF..EAEEEA
Retrocopy FVSEDQQYQDATTEEEEDFSKEAEEEA

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	0.20 RPM	376.72 RPM
SRP007412_cerebellum	0.39 RPM	279.51 RPM
SRP007412_heart	0.50 RPM	196.91 RPM
SRP007412_kidney	0.71 RPM	189.18 RPM
SRP007412_liver	0.07 RPM	550.20 RPM
SRP007412_testis	0.00 RPM	49.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2527 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2527 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3733
Gorilla gorilla	retro_ggor_2519

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000022655	4 retrocopies	retro_ggor_2388, retro_ggor_244, retro_ggor_2519, retro_ggor_2651,
Macropus eugenii	ENSMEUG00000015992	1 retrocopy	retro_meug_978,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106, retro_opri_237, retro_opri_46, retro_opri_656,
Pan troglodytes	ENSPTRG00000008496	1 retrocopy	retro_ptro_2369,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527 , retro_ptro_2677,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,