RetrogeneDB ID: retro_dord_631

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_44006:4361..5523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vps37a
• Ensembl ID: ENSDORG00000014879
• Aliases: None
• Description: vacuolar protein sorting 37A (yeast) [Source:MGI Symbol;Acc:MGI:1261835]

Sequence

>retro_dord_631
ACCAAGAGCACCTCCTTCTCCGCAGCAGGGTCCTCGGTGGTGGCCTCACCAGCCTCCAACAACAGAAGCAGTGCTTGATA
GAGTCCCTCTGGAACTCCCACTCCAGTATAGCTGAAATTCAGAAACATGTGGAATACAGATTGCCCTTCACTGTAAACAA
CTTGACAATTAACATTAATATACTACTTCCTCCACAGTTTCCTCAGGAAAAACCAGTGATCAGTGTTTATCCACCAATCC
AACATCATTTAATGGATAAACAAGTAATATATGTTACCTCTCCATTAGTAAGCAAATTTACAATGCACTCAGATCTTGAA
AAGATTAGCCAGAGTCGGTTGGATGAGTTTTGGAAGAATTCTCCTGTTCTAGCTCCCACTTCAACAGCATTTCCATACCT
GTATAGTAACCCAGGTGGGCTGCCTCCTTATGCTTTTCAGGGTTTTCCGTTTCTTCCTGCATATCCTCCTCAAGAAGCTA
ACAGAACATCACTTCTTTGTTACTGACACTGTTTCTTCTTCAACAACAAGTTACACAACAGCCAAGCCTGCTGCTCCTAC
ATTTGGTGTTCTTTCAAGTCTGCCATTGCCTGTTCCCACAATGGAAACCTCAACACCGATAAGCCAAAGTCGTTTTGGGT
AGGAGATGCCAGATGTCCCTGATGCATTTCCAGAACTCTCAGAATTGTGTCACAACTCACAGATATGAATGAACAAGAGG
AAGTATTACTAGAACAGTTTCTGTGTTTACCTCAACTAAAACAAATTATTAATGACAAGTATGATTTAGTAAAAAGTATT
GATGAATTAGCAAGAAAAATCTCCTCTTGGAGCCCAGTTTGGAAGCCAAAAGGCAAAGAGTTTTAGATAAGTATGAGTTA
CTTACACAAATGAAATCTATGTTTGAAAAGAAGATGCAGAGACAACATGAACTGAGTGAGAGTTGTAGTGCAAGTGCTCT
ACAGGCAAGATTGAAAGTCGGTGCACATGAAGCTGAGGAAGAATCTAATAATATTGCTGAAGATTTCTTGGAGGGAAAAA
CTGAAATAGATGATTTTCTCAGTAGCTTCATGGAAAAAAGAACAATTTGCCATTGTAGAAGAGCCAAGGAAGAAAAACTT
CAACAAATGATAGCAATACACAGCCAATTTCATGCTCCATTA

Alignment

ORF - retro_dord_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TKSASSSSAAGSPA-GLTSLQQQKQRLIESLRNSHSSIAEIQKDVEYRLPFTVNNLTININILLPPQFPQ
          TKS.S.S.A..S...GLTSLQQQKQ.LIESL.NSHSSIAEIQK.VEYRLPFTVNNLTININILLPPQFPQ
Retrocopy TKSTSFSAAGSSVV<GLTSLQQQKQCLIESLWNSHSSIAEIQKHVEYRLPFTVNNLTININILLPPQFPQ

Parental  EKPVISVYPPIRHHLMDKQGIYVTSPLVSNFTMHSDLGKIIQSLLDEFWKNPPVLAPTSTAFPYLYSNPS
          EKPVISVYPPI.HHLMDKQ.IYVTSPLVS.FTMHSDL.KI.QS.LDEFWKN.PVLAPTSTAFPYLYSNP.
Retrocopy EKPVISVYPPIQHHLMDKQVIYVTSPLVSKFTMHSDLEKISQSRLDEFWKNSPVLAPTSTAFPYLYSNPG

Parental  GLPPYASQGFPFLPAYPPQEANR-NITSLSVA-DTVSSSTTSYTTAKPAAPTFAVLSSLPLPVPTMETST
          GLPPYA.QGFPFLPAYPPQEANR.NITSL.......SS.T.SYTTAKPAAPTF.VLSSLPLPVPTMETST
Retrocopy GLPPYAFQGFPFLPAYPPQEANR<NITSLLLT<TVSSSTT-SYTTAKPAAPTFGVLSSLPLPVPTMETST

Parental  PISQNGFGYKMPDVPDAFPELSELSVSQLTDMN-EQEEVLLEQFLSLPQLKQIINDKDDLVKSIEELAR-
          PISQ..FG..MPDVPDAFPELSEL.......MN...E..L.EQFL.LPQLKQIINDK.DLVKSI.ELAR.
Retrocopy PISQSRFG*EMPDVPDAFPELSELCHNSQI*MN<QEEVLL-EQFLCLPQLKQIINDKYDLVKSIDELAR<

Parental  KNLLLEPSLEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAEEESDNIAED
          KNLLLEPSLEAKRQ.VLDKYELLTQMKS.FEKKMQRQHELSESCSASALQARLKV.AHEAEEES.NIAED
Retrocopy KNLLLEPSLEAKRQRVLDKYELLTQMKSMFEKKMQRQHELSESCSASALQARLKVGAHEAEEESNNIAED

Parental  FLEGKTEIDDFLSSFMEKRTICHCRRAKEEKLQQVIAMHSQFHAPL
          FLEGKTEIDDFLSSFMEKRTICHCRRAKEEKLQQ.IA.HSQFHAPL
Retrocopy FLEGKTEIDDFLSSFMEKRTICHCRRAKEEKLQQMIAIHSQFHAPL

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_631 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 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000682	2 retrocopies	retro_chof_1257, retro_chof_2124,
Callithrix jacchus	ENSCJAG00000011769	1 retrocopy	retro_cjac_1790,
Dipodomys ordii	ENSDORG00000014879	9 retrocopies	retro_dord_257, retro_dord_294, retro_dord_542, retro_dord_544, retro_dord_580, retro_dord_598, retro_dord_631 , retro_dord_668, retro_dord_751,
Homo sapiens	ENSG00000155975	1 retrocopy	retro_hsap_3256,
Gorilla gorilla	ENSGGOG00000011650	1 retrocopy	retro_ggor_2217,
Nomascus leucogenys	ENSNLEG00000002558	1 retrocopy	retro_nleu_2687,
Pongo abelii	ENSPPYG00000018386	2 retrocopies	retro_pabe_2699, retro_pabe_2821,
Pan troglodytes	ENSPTRG00000020019	1 retrocopy	retro_ptro_2202,