RetrogeneDB ID: retro_ogar_3450

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873849.1:200172..201402(+)
• Located in intron of: None

Retrocopy information

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

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_3450
GGTACCTACCACGGGGATAGCTATCTGCAGCTAGACCAAATCTCTGTGTACTACAATGAAGCCACAGGTGGCAAATATGT
TCCTTGTGCTATCCTAGTGGATCTAGAACCTGGGACCATGGACTCTGTTCGCTCAGATCCTTTTGGCCAAATCTTCAGAC
CAGACAACTTTGTTTTTGGTCAGTCTGGGGCAGGCAACAACTGGGCCAACGGCCACTATACAGAAGGGACTGAGCTGGTT
GATTCAGTCCTGGATGTGGTACAGAAGGAGGCAGAGAGCAGTGACTGCCTGCAGGGCTTCCAGCTGACCCACTCACTGGA
TGGGGGCACAGGTTCTGGAATGGGCACACTCCTTATCAGCAAGATCCGAGAAGAGTATTCTGACTGCATCATGAGTACCT
TTAGTGTGGTGCCTTCACCCAAAGTGTCTGATACCATGGTTGAGCCCTATAATGCCACCCTCTCTGTCTATCAGTTGGTA
GAGAACACTGATGAGACCTACTGCATTGACAACGAGGCCCTTTACGACATCTGCTTCTGTACCCTAAAGTTGACCACACC
AACTTATGGGGACCTGAACCACCTTGTCTCAGCCACCATGAGTGGTGTCACCACCTGCCTCCATTTCCCTGGCCAGCTCA
ATGCTGACCTTCACAAGCTGGCACTCAACACGGTACCCTTCCCACGTCTCCACTTCTTCATGCCTGGCTTTGCCCCTCTC
ACCAGCCATGGAAGCCAGCAGTATTGGGCTCTCACTGAGCCAGAACTCACCCAACAGGTCTTTGATGCCAAGAACATGAT
GGCGGCCTGTGACCCCCGCCATGGCTGATACCTCACTGTGGCTGCTGTCTTCTGTGGACGGGTGTCCATGAAGGAGGTAG
ATGAGCAGATGCTCAATGTGCAGAACAAGAATAGCAGCTACTTCATCCAATGGATCCCCAACAATGTCAAGACAGCTGTC
TGTGACATCCCACCTCGTGGCTTCAAGATGGCAGTCACCTTCATTGGCAACAGCACAGCCATCCAGGAGCTCTTCAAGCA
CATCTCAGAGCAGTTCACTGCTATGTTCCGCCAGAAGGCATTCCTCCACTGGTATACAGGCGAGGGCATGGACGAGATGG
AATTCACCGAGGCTGAGAGCAGCATGAACGACCTCGTCTCTGAGTATCAGCAGTACCAGGATGCCACCGTGGAAGAGGAG
GAGAATTTTGGTGAAGAGGCTGAAGAGGAG

Alignment

ORF - retro_ogar_3450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 92.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAK
          GTYHGDS.LQL..I.VYYNEATGGKYVP.A.LVDLEPGTMDSVRS.PFGQIFRPDNFVFGQSGAGNNWA.
Retrocopy GTYHGDSYLQLDQISVYYNEATGGKYVPCAILVDLEPGTMDSVRSDPFGQIFRPDNFVFGQSGAGNNWAN

Parental  GHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSP
          GHYTEG.ELVDSVLDVV.KEAES.DCLQGFQLTHSL.GGTGSGMGTLLISKIREEY.D.IM.TFSVVPSP
Retrocopy GHYTEGTELVDSVLDVVQKEAESSDCLQGFQLTHSLDGGTGSGMGTLLISKIREEYSDCIMSTFSVVPSP

Parental  KVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFP
          KVSDT.VEPYNATLSV.QLVENTDETYCIDNEALYDICF.TLKLTTPTYGDLNHLVSATMSGVTTCL.FP
Retrocopy KVSDTMVEPYNATLSVYQLVENTDETYCIDNEALYDICFCTLKLTTPTYGDLNHLVSATMSGVTTCLHFP

Parental  GQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTV
          GQLNADL.KLA.N.VPFPRLHFFMPGFAPLTS.GSQQY.ALT.PELTQQ.FDAKNMMAACDPRHG.YLTV
Retrocopy GQLNADLHKLALNTVPFPRLHFFMPGFAPLTSHGSQQYWALTEPELTQQVFDAKNMMAACDPRHG*YLTV

Parental  AAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISE
          AAVF.GR.SMKEVDEQMLNVQNKNSSYF..WIPNNVKTAVCDIPPRG.KM..TFIGNSTAIQELFK.ISE
Retrocopy AAVFCGRVSMKEVDEQMLNVQNKNSSYFIQWIPNNVKTAVCDIPPRGFKMAVTFIGNSTAIQELFKHISE

Parental  QFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEAEEE
          QFTAMFR.KAFLHWYTGEGMDEMEFTEAES.MNDLVSEYQQYQDAT.EEE..F.EEAEEE
Retrocopy QFTAMFRQKAFLHWYTGEGMDEMEFTEAESSMNDLVSEYQQYQDATVEEEENFGEEAEEE

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_3450 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,