RetrogeneDB ID: retro_dord_786

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_97865:1166..2483(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000005920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tuba4a
• Ensembl ID: ENSDORG00000000154
• Aliases: None
• Description: tubulin, alpha 4A [Source:MGI Symbol;Acc:MGI:1095410]

Sequence

>retro_dord_786
ATGCGTGAGTGTCTTTCCATCCATGTGGGCCAGGCTGGTGTCCAGATTGGCAATGCCTGTGGAGAGCTCTACTGCCTGGA
ACACGGCATCCAGCCTGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCA
GTGAGACAGGCTCTGGCAAGCATGTGCCCAGGGCAGTGCTTGTAGACCTGGAGCCCACAGTCATTGATGAAGTTCGAACT
GGCACCTACCGTCAACTTTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAGTAGCTATGCCCATGGTCA
CTACACCATTGGCAAGATCATTGATCTCGTCTTGGACAAATTCGGAAGCTGGCTGACCAGTGCACAGGTCTTCAGGGTTT
CCTGGTCTTCCACAGCTTTGGTGGAGGAACGGGCTCTGGCTTCACCTCCTTGCTTGATGGAGCGTCTCTCTGTGGACTAT
GGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCGGACCCCCAGGTGTCCACAGCTGTAGTTGAGCCCTACAACTCTAT
CCTCACTACCCATACCACCCTGCAGCACTCTGATTATGCCTTCATGGTGGACAATGAGGCCATCTATGACATCTGTTGTA
GAAACCTCGATATTGAACGCCCCAACCTACACTAACCTGAACCGCCTAATTAGCCAGATTGTGTCTTCCATCACAGCTTC
ACTGAGATTTGATGGGCCCTGAATGTTGACCTGACAGAATTCCAGACCAACCTGGTGCCCTATTCCCACATCCACTTCCC
CCATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCTTGCTTTGAGC
CAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGTAAATACATGGCCTGCTGCCTGTTGTACCGTGGTGATGTGGTT
CCCAAAGATGTTAATGCTGCCATTGCCACCATCAAGACCAAGCGCAGCATCCAGTTTGTGGATTGGTGTCCCACTGGTTT
CAAGGTTGGCATCAATTACCAGCCTCCCACTGTGGTTCCTGGTGGAGACCTGGCCAAGGTGCAGCGCGCTGTGTGCATGC
TGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGCCAAGCGTGCCTTT
GTCCACTGGTATGTGGGTGAGGGGATGGAGGAAGGAGAGTTTTCTGAGGCCTGTGAGGACATGGCTGCCCTAGAGAAGGA
TTATGAGGAGGTTGGTGTGGATTCTGTGGAAGGCGAG

Alignment

ORF - retro_dord_786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDL
          MREC.S.HVGQAGVQ.GNAC.ELYCLEHGIQPDGQMPSDKTIGGGDDSF.TFF.ETG.GKHVPRAV.VDL
Retrocopy MRECLSIHVGQAGVQIGNACGELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGSGKHVPRAVLVDL

Parental  EPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDR-IRKLSDQCTGLQGFLVFH
          EPTVIDE.R.G.YRQLFHPEQLITGKEDAA..YA.GHYTIGK.IID.VLD..IRKL.DQCTGLQGFLVFH
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAASSYAHGHYTIGK-IIDLVLDK<IRKLADQCTGLQGFLVFH

Parental  SFGGGTGSGFTSLL-MERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEA
          SFGGGTGSGFTSLL.MERLSVDYGKKSKLEFSIYP.PQVSTAVVEPYNSILTTHTTL.HSD.AFMVDNEA
Retrocopy SFGGGTGSGFTSLL>MERLSVDYGKKSKLEFSIYPDPQVSTAVVEPYNSILTTHTTLQHSDYAFMVDNEA

Parental  IYDICRRNLDIERP-TYTNLNRLISQIVSSITASLRFDG-ALNVDLTEFQTNLVPYPRIHFPLATYAPVI
          IYDIC.RNLDIERP.TYTNLNRLISQIVSSITASLRFDG.ALNVDLTEFQTNLVPY..IHFP....APVI
Retrocopy IYDICCRNLDIERP>TYTNLNRLISQIVSSITASLRFDG<ALNVDLTEFQTNLVPYSHIHFP---HAPVI

Parental  SAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKTKRSIQFVDW
          SAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIA.IKTKRSIQFVDW
Retrocopy SAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDW

Parental  CPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEG
          CPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEG
Retrocopy CPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEG

Parental  EFSEAREDMAALEKDYEEVGIDSYEDE
          EFSEA.EDMAALEKDYEEVG.DS.E.E
Retrocopy EFSEACEDMAALEKDYEEVGVDSVEGE

Legend:

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

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_786 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786 ,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,