RetrogeneDB ID: retro_dord_544

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_29583:132..851(-)
• 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_544
GGTTTTCCATTTCTTCCAGCATATCCTCCTCAAGAAGTTAACAGAACATCACTTCTTTGTTACTGACACTGTTTCTTCTT
CAACAAGTTATACAACAGCCAAGTCTGCTGCTCCTACATTTGGTGTCCTTTCAAGTCTGCCATTGCCTGTTCCCACAATG
GAAACTTCAACACCGATAAGCCAAAATGGTTTTGGGTACAAGATGCCAGATGTCCCTGATGCATTTCCAGAACTCTCAGG
ATTGTGTCACAACTCACAGATATGAATGAACAAGAGGAAGTATTACTAGAACAGTTTCTGAGTTTACCTCAACTAAAACA
AATTATTAATGACAAGGGTGATTTAGTAAAAAGTATTGAGGAATTAGCAAGAAAACTCTCCTCTTGGAGCCCAGTTTGGA
AGCCAAAAGGCAAACTGTTTTAGATAAGTATGAGTTACTTACACAAATGAAATCTACGTTTGAAAAGAAAATGCAGAGAC
AACATGAACTGAGTGAGAGTTGTAGTGCAAGTGCCCTACAGGCAAGATGGAAAGTCGCTGCACATGAAGCTGAGGAAGAA
TCTGATAATATTGCTGAAGATTTCTCGGAGGGAAAAACTGAAATAGATGATTTTCTCAGTAGCTTCATGGAAAAAAGAAC
AGTTTGCCACTGTAGAAGAGCCAAGGAAGAGAAACTTAAACAAGTGATAGCAATGCACAGCCAACTTCATGGTCCATTA

Alignment

ORF - retro_dord_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 62.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFPFLPAYPPQEANRNITSLS-VADTVSSSTTSYTTAKPAAPTFAVLSSLPLPVPTMETSTPISQNGFGY
          GFPFLPAYPPQE.NR..TSL..V.DTVSSST.SYTTAK.AAPTF.VLSSLPLPVPTMETSTPISQNGFGY
Retrocopy GFPFLPAYPPQEVNR--TSLL>VTDTVSSST-SYTTAKSAAPTFGVLSSLPLPVPTMETSTPISQNGFGY

Parental  KMPDVPDAFPELSELSVSQLTDMN-EQEEVLLEQFLSLPQLKQIINDKDDLVKSIEELAR-KNLLLEPSL
          KMPDVPDAFPELS.L.......MN...E..L.EQFLSLPQLKQIINDK.DLVKSIEELAR.K.LLLEPSL
Retrocopy KMPDVPDAFPELSGLCHNSQI*MN<QEEVLL-EQFLSLPQLKQIINDKGDLVKSIEELAR<KTLLLEPSL

Parental  EAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAEEESDNIAEDFLEGKTEID
          EAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQAR.KVAAHEAEEESDNIAEDF.EGKTEID
Retrocopy EAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARWKVAAHEAEEESDNIAEDFSEGKTEID

Parental  DFLSSFMEKRTICHCRRAKEEKLQQVIAMHSQFHAPL
          DFLSSFMEKRT.CHCRRAKEEKL.QVIAMHSQ.H.PL
Retrocopy DFLSSFMEKRTVCHCRRAKEEKLKQVIAMHSQLHGPL

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_544 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,