RetrogeneDB ID: retro_ggor_2519

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:56851261..56852591(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSGGOG00000022655
• Aliases: None
• Description: None

Sequence

>retro_ggor_2519
ATGAAGGAAATTGTGCACATCCAAGCCAGTCACTGTGGCAACCAGATCGGTGCCAAGTTCTGGGAGGTGATCAGTGATGA
ACATGGCATCAACCCACCGGCACCTACCACAGGGACAGCGCCCTGCAGCTGGACCGCATCTCCGTGTACTACAATGAAGC
CACAGGTGGCAAATATGTTCCTCACGCCATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGTTCACTCAGGTCCTT
TTGGCCAGATCTTTAGACCAGACAACTTTGCTTCTGATCAGTCTGGGGCAGGCAACAACTGGGCCAAATGCCACTACACA
GAGGGGGCTGAGCTGGTTTATTTGGTCCTGGATTTGGTATGGAAGGAGGCGGAGAGCTGTGACTGCCTTCAGGGCTTCCA
GCTGACCCACTCACTTGACTGGGACACAGGCTCTGGAATTGGCACTCTCCTTATGAGCAAGATCCAAGAAGAGTACCCTG
ATTGCTTCATGAATACCTTCAGTGTGGGTACCTTCACACAAGGTATCTGACACCGTGGTTGAGCCGTACAATGCCACCCT
CTCCGTCCATCAGTTGGTAGAGAACACTGATGAGACCTATTGCATTGACAATGAGGCCCTCTAGGATATCTGCTTCCGCA
ATCTGAAGCTGACCACACCAACCTACTGGGATCTGAACTACCTCGTCTTAGCCACCATGAGTGGTGTCACCACCTGCCTC
CACTTCCTGGCCAGCTCAGTGCTGACCTCTGCAAGTTGGCAGTCAACATGGTTCCCTTCCCATATCTCCATTTCTTTATG
CCTGGCTTTGCCCCTTTCACCAGCCGTGGAAGCCAGTAATATCAAGCTCTCACCGTGCCCCAACTTACCCAGCGGGTCTT
TGATGCCAAAAACCTGATGGCTGCTTGTGACCCCCGCCACGGCCGATACCTCACCATGGCTGCTGTCTCCAGTGGTCGGA
TGTCCATGAAGGAGGTCAATGAGCAGATGCTCAAAGTGCAGAACAAGAACAGCAGCTACTTTGTGGAATGGATCCCCAAC
AACATCAAGACAGCTGTCTGTGACATCCACCTCATGGCCTCAAGATGGCTGTCACCTTCATCGGAAACAGCACTGGCATC
CAGTAGCTCTTCAAGCGCATCTCGGAGCAGTTCACTGCCATGTTCTACCAGAAGGCCTTCCTCCACTGCTACACAGGCGA
GGGCATGGATGAGATGGAGTTCACTGAGGCTGAGAGCAACATGAACAACTTCGTCTCTGAGGATCAGCAGTACCAGGATG
CTACCACAGAAGGGGAAGAGGATTTCGGTAAGGAGGCTGAAGAGGAGGCC

Alignment

ORF - retro_ggor_2519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

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

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          PGTMDSV.SGPFGQIFRPDNF...QSGAGNNWAK.HYTEGAELV..VLD.V.KEAESCDCLQGFQLTHSL
Retrocopy PGTMDSVHSGPFGQIFRPDNFASDQSGAGNNWAKCHYTEGAELVYLVLDLVWKEAESCDCLQGFQLTHSL

Parental  GGGTGSGMGTLLISKIREEYPDRIMNTFSV-VPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          ...TGSG.GTLL.SKI.EEYPD..MNTFSV.VPS.KVSDTVVEPYNATLSVHQLVENTDETYCIDNEAL.
Retrocopy DWDTGSGIGTLLMSKIQEEYPDCFMNTFSV>VPSHKVSDTVVEPYNATLSVHQLVENTDETYCIDNEAL*

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRF-PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRG
          DICFR.LKLTTPTY.DLN.LV.ATMSGVTTCL.F.PGQL.ADL.KLAVNMVPFP.LHFFMPGFAP.TSRG
Retrocopy DICFRNLKLTTPTYWDLNYLVLATMSGVTTCLHF<PGQLSADLCKLAVNMVPFPYLHFFMPGFAPFTSRG

Parental  SQQYRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPN
          SQ.Y.ALTVP.LTQ.VFDAKN.MAACDPRHGRYLT.AAV..GRMSMKEV.EQML.VQNKNSSYFVEWIPN
Retrocopy SQ*YQALTVPQLTQRVFDAKNLMAACDPRHGRYLTMAAVSSGRMSMKEVNEQMLKVQNKNSSYFVEWIPN

Parental  NVKTAVCDI-PPRGLKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMN
          N.KTAVCDI.PP.GLKMAVTFIGNST.IQ.LFKRISEQFTAMF..KAFLH.YTGEGMDEMEFTEAESNMN
Retrocopy NIKTAVCDI<PPHGLKMAVTFIGNSTGIQ*LFKRISEQFTAMFYQKAFLHCYTGEGMDEMEFTEAESNMN

Parental  DLVSEYQQYQDATAEEEEDFGEEAEEEA
          ..VSE.QQYQDAT.E.EEDFG.EAEEEA
Retrocopy NFVSEDQQYQDATTEGEEDFGKEAEEEA

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	0.00 RPM	302.16 RPM
SRP007412_cerebellum	0.00 RPM	211.45 RPM
SRP007412_heart	0.00 RPM	106.69 RPM
SRP007412_kidney	0.08 RPM	102.02 RPM
SRP007412_liver	0.29 RPM	176.52 RPM
SRP007412_testis	0.73 RPM	156.23 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2519 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3733
Pan troglodytes	retro_ptro_2527

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000002192	1 retrocopy	retro_ggor_2364,
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	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,