RetrogeneDB ID: retro_meug_157

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_4660:83312..84290(+)
• Located in intron of: ENSMEUG00000008413

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSMEUG00000011167
• Aliases: None
• Description: tubulin, alpha 1b [Source:HGNC Symbol;Acc:18809]

Sequence

>retro_meug_157
ATGCATGAGTATATCTCCATCCATGTTGGCCAGGCTGGAGTGCAGATGGGCAATGTGTGCTGGAAAATATGTTGCTTACA
GCATGGTATTGAACCCAATGGTACCATGTCCAGTGACAGGATCTTGGAGGGGGGTGGTGATTCTTTCAATACCTTCTTCA
GTGAGACTGGAGCTGGCAAATATGTTCCCAGAGTGCTCTTTGTACACTTTGAGCCTTCAGTAATAGATGAGGTTCTGACT
AGAATCTATAAACAGCTATTCCCTCTAAGCAGCTGATCTCTGGCAAGGAGGATGTTGCTAATAACTATACCCGGGGCCAT
TACACTGTGGGGAAGGAAATAATTGATCATGTATTGGAGCACATCTGAAAACTGTCAGACCAATGCACAGGGCTACAGGG
ATTCCTGACATTTCACAGCTTTGGGGGCAGCACAAGGTCAGGTTTCACCTCTCTGCTGATGGAGAGGCTCTCTGTTGACT
GTGACAAGAAGTCCAAGATGGAGTTTGCCATCTACCCCGACCCACAAGTATTCACCCATTATAGGGCTGTAGTGGAGCCC
TATAATTCAATCCTAACCATTCACACCACACTGGAGCACTCAGACTGTGCCTTTATGGTGGACAATGAAGCAACATATAA
CATGTGCCACTGGAACCTGGATTTTGAGTGCCCAACATACACCAACCTCAACCAGCTCATTGACCAGATTGTTTCCTCCA
TCGCTGCCTCCCTGCACTTTGACGGTGCCCTCAATGTAGACCTCATGGAGTTCCAGATCAACCTGGTACCTTATCCTCAA
ATCAACTTCCCCCTCGTCACCTACTCACTCATTATCTCTGCTGAAAAGGCCTATCACAAACAGCTCTCCATAGCAGAGAT
CTCCAATGCTGGGCTTTGACCCCTCCAACCAGATGGTACAGTATGACCCATGTCATGGCAAGTACATGGCCTATTGCATG
CAGTATTGAGGTGATGTC

Alignment

ORF - retro_meug_157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.78 %
• Parental protein coverage: 71.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          M.E.ISIHVGQAGVQ.GN.CW...CL.HGI.P.G.M.SD....GG.DSFNTFFSETGAGK.VPR..FV..
Retrocopy MHEYISIHVGQAGVQMGNVCWKICCLQHGIEPNGTMSSDRILEGGGDSFNTFFSETGAGKYVPRVLFVHF

Parental  EPTVIDEVRTGTYRQLFH-PEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          EP.VIDEV.T..Y.QLF....QLI.GKED.ANNY.RGHYT.GKEIID.VL..I.KL.DQCTGLQGFL.FH
Retrocopy EPSVIDEVLTRIYKQLFP<SKQLISGKEDVANNYTRGHYTVGKEIIDHVLEHI*KLSDQCTGLQGFLTFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVST---AVVEPYNSILTTHTTLEHSDCAFMVDN
          SFGG.T.SGFTSLLMERLSVD..KKSK.EF.IYP.PQV.T...AVVEPYNSILT.HTTLEHSDCAFMVDN
Retrocopy SFGGSTRSGFTSLLMERLSVDCDKKSKMEFAIYPDPQVFTHYRAVVEPYNSILTIHTTLEHSDCAFMVDN

Parental  EAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVI
          EA.Y..C..NLD.E.PTYTNLN.LI.QIVSSI.ASL.FDGALNVDL.EFQ.NLVPYP.I.FPL.TY...I
Retrocopy EATYNMCHWNLDFECPTYTNLNQLIDQIVSSIAASLHFDGALNVDLMEFQINLVPYPQINFPLVTYSLII

Parental  SAEKAYHEQLSVAEITNA-CFEPANQMVKCDPRHGKYMACCLLYRGDV
          SAEKAYH.QLS.AEI.NA..F.P.NQMV..DP.HGKYMA.C..Y.GDV
Retrocopy SAEKAYHKQLSIAEISNA>GFDPSNQMVQYDPCHGKYMAYCMQY*GDV

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_157 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_157 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157 , retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,