RetrogeneDB ID: retro_dord_668

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_50120:9984..10697(-)
• 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_668
ACCAAGAGCACCTCCTTCTCCACAGCAGGGTCCCCGGTGGTGGCCTCACCAGCCTCCAACAGCAGAAGCAGCGCTTGATC
GAGTCCCCCAGAATTCCCACTCCAGTATAGCTGAAATTCAGAATGATGTGGAATACAGATTGCCCTTCACTGTAAACAAC
TTGACAATTAACATTAATATACTACTTCCTCCACAGTTTCCTTAGGAAAAAACAGTGATCAGTGTTTATCCACCAATCCG
ACATCCTTTAATGGATAAACAAGGAATATATGTTACCTCTCCATTAGTAAGCAATTTTACAATGCACTCAGATCTTGGAA
AGATTAGCCAGAGTCTGTTGGATGAGTTTTGGAAGAATTCTCCTGTTTTAGCTCCCACTTCAACAGCATTTCCATACCTG
TATAGTAACCCAGGTGGACTGCTTCCTTATGCTTCTCAGTGTTTTCCGTTTCTTCCTGCATATCCTCCTCAAGAAGCTAA
CAGAACATCACTTCTCTGTTACTGACACTGTTTCTTCTTCAACAAGTTATACAACAGCCAACTCTGCTCTCCTACATTTG
GTGTCCTTTCAAGTCTGCCATTGCCTGTTCCCACAATGGAAACTTCCAACACCGATAAACCAAAATGGTTTTGGGTAAAA
GATGCCAGATGTCCCTGATGCATTTCCAGAACTCTCAGAATTAAGTGTGTCACAACTCACAGATATGAATGAG

Alignment

ORF - retro_dord_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.59 %
• Parental protein coverage: 61.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TKSASSSSAAGSPA-GLTSLQQQKQRLIESLR-NSHSSIAEIQKDVEYRLPFTVNNLTININILLPPQFP
          TKS.S.S.A......GLTSLQQQKQRLIES.R.NSHSSIAEIQ.DVEYRLPFTVNNLTININILLPPQFP
Retrocopy TKSTSFSTAGSPVV<GLTSLQQQKQRLIESPR<NSHSSIAEIQNDVEYRLPFTVNNLTININILLPPQFP

Parental  QEKPVISVYPPIRHHLMDKQGIYVTSPLVSNFTMHSDLGKIIQSLLDEFWKNPPVLAPTSTAFPYLYSNP
          .EK.VISVYPPIRH.LMDKQGIYVTSPLVSNFTMHSDLGKI.QSLLDEFWKN.PVLAPTSTAFPYLYSNP
Retrocopy *EKTVISVYPPIRHPLMDKQGIYVTSPLVSNFTMHSDLGKISQSLLDEFWKNSPVLAPTSTAFPYLYSNP

Parental  SGLPPYASQGFPFLPAYPPQEANRNITSL-SVADTVSSSTTSYTTAKPA-APTFAVLSSLPLPVPTMETS
          .GL.PYASQ.FPFLPAYPPQEANR..TSL.SV.DTVSSST.SYTTA..A..PTF.VLSSLPLPVPTMETS
Retrocopy GGLLPYASQCFPFLPAYPPQEANR--TSL>SVTDTVSSST-SYTTANSA<SPTFGVLSSLPLPVPTMETS

Parental  -TPISQNGFGYKMPDVPDAFPELSELSVSQLTDMNE
          .TPI.QNGFG.KMPDVPDAFPELSELSVSQLTDMNE
Retrocopy >TPINQNGFG*KMPDVPDAFPELSELSVSQLTDMNE

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_668 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,