RetrogeneDB ID: retro_ogar_3410

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873821.1:137950..139196(+)
• Located in intron of: ENSOGAG00000002968

Retrocopy information

• Ensembl ID: ENSOGAG00000008311
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUBB4B
• Ensembl ID: ENSOGAG00000005927
• Aliases: None
• Description: tubulin, beta 4B class IVb [Source:HGNC Symbol;Acc:20771]

Sequence

>retro_ogar_3410
ATGAGGGAAATCGTGCACATCCAGGCCAGTCAGTGTGGTAACCAAATTGGTGCCAAGTTCTAGGAGGTGATCAGCGATGA
ACACGGCATCGACCCCACCAGTACCTACGGGGATGGCGATCTGCAGCTAGACCCAATCTCTGTGTACTACAATGAAGCCA
CAGGTGGCAAATATGTTCCTCGTGCTATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGTTCGCTCAGGTCCTTTT
GGCCGAGTCTTTAGACCAGACAACTTTGTTTTTGGTCAGTTTGGGGCAGGCAACAACTGGGCCAAGGGCCACTATACAGA
AGGGGCTGAGCTGGTTGATTCAGTCCTGGATGTGGTACAAAAGGAGGCAGAGAGCTGTGGCTGCCTGCAGGGCTTCCAAC
TGACCCGCTCGCTGGATGGGGATACAGGTTCTGAAATGGGCACATTCCTTATCAGCAAGATCCAAGAAGAGTATTCTGAC
TGCATCATGAATACCTTTAGTGTGGTGCCTTCACCCAAAGTGTCTGATACTGTGGTTGAGCCCTATAATGCCACCCTCTC
TGTCTATCAGTTGGTAGAGAACACTGATGAGACCTACTGCACTGACAACGAGGCCCTTTACGACATCTGCTTCCGTACCC
TAAAGTTGACCACGCCAACTTATGGGGACCTGAACCACCTTGTCTCAGCCACCATGAGTGGTGTCACCGCCTGCCTCCAT
TTCCATGGCCAGCTCAACACTGACCTCCACAAGCTGGCAGTCAACATGGTGCCCTTCCCAGGTCTCCACTTCTTCATCTG
GCTTTGCCCCTCTCACTGCCATGGAAGCCAGCAGTATTGGGCTCTCACTGAGCCAGAACTCACCCAGCAGGTCTTCGATG
CCAAGAACATGATGGCTGCCTGTGACCCCGCCATGGCCGATACCTCACCATGGCTGCTGTCTTCCTTGGACGGATGTCCA
TGAAGGAGGTAGATGAGCAGATGCTCAATGTGCAGAACAAGAATAGCAGCTACTTCGTGGACGGATCCCCAATAATGTTG
AGATAGCTGTCTGCGACATCCCGCCTCGTGGCCTCAAGATGGCAGTCACCTTCACTGGCAACAGCACAGCCATCCAGGAG
CTCTTCAAGCACATCTCAGAGCAGTTCACTGCCATGTTCCACCGGAAGGCCCTCCCCCACTGGTATACAGGCGAGGGCAT
GGACGAGATGGAATTCACCGAGGCTGAGAGCAACATGAACAACCTG

Alignment

ORF - retro_ogar_3410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.95 %
• Parental protein coverage: 93.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          MREIVH.QA.QCGNQIGAKF.EVISDEHGIDPT.TY.GD.DLQL..I.VYYNEATGGKYVPRA.LVDLEP
Retrocopy MREIVHIQASQCGNQIGAKF*EVISDEHGIDPTSTY-GDGDLQLDPISVYYNEATGGKYVPRAILVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDSVRSGPFG..FRPDNFVFGQ.GAGNNWAKGHYTEGAELVDSVLDVV.KEAESC.CLQGFQLT.SL.
Retrocopy GTMDSVRSGPFGRVFRPDNFVFGQFGAGNNWAKGHYTEGAELVDSVLDVVQKEAESCGCLQGFQLTRSLD

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          G.TGS.MGT.LISKI.EEY.D.IMNTFSVVPSPKVSDTVVEPYNATLSV.QLVENTDETYC.DNEALYDI
Retrocopy GDTGSEMGTFLISKIQEEYSDCIMNTFSVVPSPKVSDTVVEPYNATLSVYQLVENTDETYCTDNEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKLTTPTYGDLNHLVSATMSGVT.CL.F.GQLN.DL.KLAVNMVPFP.LHFF.....P....GSQQ
Retrocopy CFRTLKLTTPTYGDLNHLVSATMSGVTACLHFHGQLNTDLHKLAVNMVPFPGLHFFI-WLCPSHCHGSQQ

Parental  YRALTVPELTQQMFDAKNMMAACD-PRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEW-IPNN
          Y.ALT.PELTQQ.FDAKNMMAACD.PRHGRYLT.AAVF.GRMSMKEVDEQMLNVQNKNSSYFV...IPNN
Retrocopy YWALTEPELTQQVFDAKNMMAACD<PRHGRYLTMAAVFLGRMSMKEVDEQMLNVQNKNSSYFVDG<IPNN

Parental  VKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
          V..AVCDIPPRGLKM..TF.GNSTAIQELFK.ISEQFTAMF.RKA..HWYTGEGMDEMEFTEAESNMN.L
Retrocopy VEIAVCDIPPRGLKMAVTFTGNSTAIQELFKHISEQFTAMFHRKALPHWYTGEGMDEMEFTEAESNMNNL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3410 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410 , retro_ogar_3450,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,