RetrogeneDB ID: retro_dord_420

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_176128:421..1114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam58b
• Ensembl ID: ENSDORG00000012846
• Aliases: None
• Description: family with sequence similarity 58, member B [Source:MGI Symbol;Acc:MGI:1916359]

Sequence

>retro_dord_420
GGGGTGGCAGGGTCGGAGCCCAGGGTGCACTTCCGAGTGACAAGGTTCATCATGGAGGCAGGTGTCAAGCTAGCTATGCG
CTCCATTCCCATCGCCACTGCCTGCACCATCTACCATAAGTTCTTTCGCGAGATCAGCCTGGAGGCTTATGACCCTTACC
TCGTCGCCATGTCATCCATTTACTTGGCGGGCAAGGTGGAGGAGCAGCATCTGCGAATCAGAGACATCATCAATGTATCC
AACAGCTACTTCCACCCAGGCAGCGAGCCCTTGGAGCTGGACTCGCGCTTCTGGGAGCTCCGGGATAGCGTTGTGCAGTG
TGAGCTCCTTGTGCTGAGGGCCCTGCGCTTCCAGGTCTCCTTCCAGCACCCGCACAAGTACCTGCTCCACTATCTGATGG
CCCTCAAACACTGGCTGAATCGGTACAGCTGGCAGCGGACTCCTGTTGCCATCGTGGCCTGGGCCTTGCTGCGGGACAGC
TACCACGGGGGGCTGTGCCTTCGCTTCCAGCCTCAGCACCTGGCCGTGGCTGTGCTCTACCTGGCCCTACAGGTCTATGG
AGTAGAAGTCCCTGCTGAGGAGGAGGCCGAGAAGCCATGGTGGCAGGTGTTTAGTGAAGACCTTACCAAGCCAATCATTG
ATAACATTGTGTCTGATCTCATTCAGATTTATGCCATGGACACAGAGATCCCT

Alignment

ORF - retro_dord_420 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLPVPKARVHFEVTKFIMEAGIKLGMRSIPIATACTIYHKFFGEVNLDAYDPYLVAISSIYLAGKVEEQH
          G......RVHF.VT.FIMEAG.KL.MRSIPIATACTIYHKFF.E..L.AYDPYLVA.SSIYLAGKVEEQH
Retrocopy GVAGSEPRVHFRVTRFIMEAGVKLAMRSIPIATACTIYHKFFREISLEAYDPYLVAMSSIYLAGKVEEQH

Parental  LRTRDIINVSNRHFNPGSKPLELNSRFWALRDSIVQCELLILRVLRFQVSFQHPHKYLLHYLISLKNWLN
          LR.RDIINVSN..F.PGS.PLEL.SRFW.LRDS.VQCELL.LR.LRFQVSFQHPHKYLLHYL..LK.WLN
Retrocopy LRIRDIINVSNSYFHPGSEPLELDSRFWELRDSVVQCELLVLRALRFQVSFQHPHKYLLHYLMALKHWLN

Parental  RYTWQRTPISVTAWALLRDSYHGGLCLRFQAQHLAVAVLYLALHIYGVEVPAESESEKPWWQVLSDDLTK
          RY.WQRTP....AWALLRDSYHGGLCLRFQ.QHLAVAVLYLAL..YGVEVPAE.E.EKPWWQV.S.DLTK
Retrocopy RYSWQRTPVAIVAWALLRDSYHGGLCLRFQPQHLAVAVLYLALQVYGVEVPAEEEAEKPWWQVFSEDLTK

Parental  PIIDNIVSDLIQIYSMDTGIP
          PIIDNIVSDLIQIY.MDT.IP
Retrocopy PIIDNIVSDLIQIYAMDTEIP

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_420 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Dipodomys ordii	ENSDORG00000012846	1 retrocopy	retro_dord_420 ,
Gorilla gorilla	ENSGGOG00000027073	2 retrocopies	retro_ggor_2302, retro_ggor_911,
Macaca mulatta	ENSMMUG00000011480	1 retrocopy	retro_mmul_557,
Nomascus leucogenys	ENSNLEG00000013298	2 retrocopies	retro_nleu_1493, retro_nleu_2416,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,