RetrogeneDB ID: retro_dord_542

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_29570:8105..9258(+)
• 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_542
AGCACCTCCTTCTCCACAGCAGGGTCCCTGGTGGTGTCCTCACCAGCCTCCAACAGCAGAAGCAGTGCTTGATCGAGTCC
CTCCGGAACTCCCACTCCAGTATAGCTGAAATACAGAAAGATGTGAAATACAGATTGCCCTTCACTGTAAACAACTTGAC
AATTAACATTAATATAGTACTTCCTCCACATTTTCCTCAGGAAAATCCAGCGATCAGTGTTTATCCAACAATCTGACATC
GTTTAATGGATAAACAAGGAATATATGTTACCTCTCCATTAGTAAGCAATTTTACAATACACTCAGATCTTGGAAAGATT
AGCCAGAGTCTGTTGGATGAGTTTTGGAAGAATTTTCCTGTTTTAGCTCCCACTTCAACAGCATTTCCATACCTGTATAG
TAACCCAGGTGGGCTGCCTCCTTATGCTTCTTAGGGTTTTCCATTTCTTCCTGCATATCCTCCTCAAGAAGCTTACAGAA
CATCACTTCTTTGTTACTGACACTGTTTCTTCTTCAACAAGTTATACAACAGCCAAGTCTGCTGCTCCTACATTTGGTGT
CCTTTCAAGTCTGCCATTGCCTGTTCCCACAATGGAAACTTCAACACCGATAAGCCAAAATGGTTTTGGTCACAAGATGC
CAGATGTCCCTGATGCATTTCCAGAACTCTCAGAATTGTGTCACAACTCACAGATATGAATGAACAAGAGGAAGTATTAC
TAGAACAGTTTCTGAGTTTACCTCAACTAAAACAAATTATTAATGACAAGGGTGATTTAGTAAAAAGTATTGAAGAATTA
GCAAGAAAAATCTCCTCTTGGAGCCCAGTTTGGAAGCCAAAAGGCAAACTGTTTTAGATAAGTATGAGTTACTTTCACAA
ATGAAATCTACGTTTGAAAAGAAGATGCAGAGACAACATGAACTGAGTGAGAGTTGTAGTGCAAGTGCCCTACAGGCAAG
ATGGAAAGTCGCTGCACATGAAGCTGAGTAAGAATCTGATAATATTGCTGAAGATTTCTCAGAGGGAAAAACTGAAATAG
ATGATATTCTCAGTAGCTTCATGGAAAAAAGAACAGTTTGCCACTGTAGAAGAGCCAAGGAAGAGAAACTTAAACAAGTG
ATAGCAATGCACAGCCAACTTCATGGTCCATTA

Alignment

ORF - retro_dord_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 99.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASSSSAAGS-PAG-LTSLQQQKQRLIESLRNSHSSIAEIQKDVEYRLPFTVNNLTININILLPPQFPQEK
          ..S.S.AGS.P.G.LTSLQQQKQ.LIESLRNSHSSIAEIQKDV.YRLPFTVNNLTININI.LPP.FPQE.
Retrocopy STSFSTAGS<PGGVLTSLQQQKQCLIESLRNSHSSIAEIQKDVKYRLPFTVNNLTININIVLPPHFPQEN

Parental  PVISVYPPIRHHLMDKQGIYVTSPLVSNFTMHSDLGKIIQSLLDEFWKNPPVLAPTSTAFPYLYSNPSGL
          P.ISVYP.I.H.LMDKQGIYVTSPLVSNFT.HSDLGKI.QSLLDEFWKN.PVLAPTSTAFPYLYSNP.GL
Retrocopy PAISVYPTI*HRLMDKQGIYVTSPLVSNFTIHSDLGKISQSLLDEFWKNFPVLAPTSTAFPYLYSNPGGL

Parental  PPYASQGFPFLPAYPPQEANRNITSLS-VADTVSSSTTSYTTAKPAAPTFAVLSSLPLPVPTMETSTPIS
          PPYAS.GFPFLPAYPPQEA.R..TSL..V.DTVSSST.SYTTAK.AAPTF.VLSSLPLPVPTMETSTPIS
Retrocopy PPYAS*GFPFLPAYPPQEAYR--TSLL>VTDTVSSST-SYTTAKSAAPTFGVLSSLPLPVPTMETSTPIS

Parental  QNGFGYKMPDVPDAFPELSELSVSQLTDMN-EQEEVLLEQFLSLPQLKQIINDKDDLVKSIEELAR-KNL
          QNGFG.KMPDVPDAFPELSEL.......MN...E..L.EQFLSLPQLKQIINDK.DLVKSIEELAR.KNL
Retrocopy QNGFGHKMPDVPDAFPELSELCHNSQI*MN<QEEVLL-EQFLSLPQLKQIINDKGDLVKSIEELAR<KNL

Parental  LLEPSLEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAEEESDNIAEDFLE
          LLEPSLEAKRQTVLDKYELL.QMKSTFEKKMQRQHELSESCSASALQAR.KVAAHEAE.ESDNIAEDF.E
Retrocopy LLEPSLEAKRQTVLDKYELLSQMKSTFEKKMQRQHELSESCSASALQARWKVAAHEAE*ESDNIAEDFSE

Parental  GKTEIDDFLSSFMEKRTICHCRRAKEEKLQQVIAMHSQFHAPL
          GKTEIDD.LSSFMEKRT.CHCRRAKEEKL.QVIAMHSQ.H.PL
Retrocopy GKTEIDDILSSFMEKRTVCHCRRAKEEKLKQVIAMHSQLHGPL

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_542 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,