RetrogeneDB ID: retro_dord_520

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_25943:1873..2353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kras
• Ensembl ID: ENSDORG00000011469
• Aliases: None
• Description: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog [Source:MGI Symbol;Acc:MGI:96680]

Sequence

>retro_dord_520
ATGATTGAATATAAACTTGTGGTAGTTGGAGCTGGTGACGTAGGCAAAAGTGCTTTGAAGATTGAGCTAATTCAAAATCA
CTTTGTGGATGAATATGACCCACCCATAGAGGATTCCTACAGACAACAAGTAATAATTGATGGAGAAACCTGTCTCCTGG
ACATTCTCGACACAGCAAGTCAAGAGGAATGCAGTACAATGAAGGACCAGTACATGAAGCCTGGGGAGGGCTTTCTGTAT
GTATTTGCCATAAGTAATACTAAGTCATTTGAAGATATTTACCATTATAGAGAACAAATTAAAAGAGTCAAAGACTCTGA
AGATGTACCTATGGTTCTAATAGGAAATAAATGTAATTTGCCTTTGAGAACAGTAGACAAAAAGCAGGCTCAGGATTTAG
CAAGAAGTTATGGAATTCCTTTCATTAAGACCTCAGCAAAGACAAGACAGGGTGTGGACAATGTTTTCTATACATCAGTT

Alignment

ORF - retro_dord_520 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 84.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGV-KSALTIQLIQNHFVD-YDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          M.EYKLVVVGAG.V.KSAL.I.LIQNHFVD.YDP.IEDSYR.QV.IDGETCLLDILDTA.QEE.S.M.DQ
Retrocopy MIEYKLVVVGAGDVGKSALKIELIQNHFVDEYDPPIEDSYRQQVIIDGETCLLDILDTASQEECSTMKDQ

Parental  YMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIP
          YM..GEGFL.VFAI.NTKSFEDI.HYREQIKRVKDSEDVPMVL.GNKC.LP.RTVD.KQAQDLARSYGIP
Retrocopy YMKPGEGFLYVFAISNTKSFEDIYHYREQIKRVKDSEDVPMVLIGNKCNLPLRTVDKKQAQDLARSYGIP

Parental  FIETSAKTRQRVEDAFYTLV
          FI.TSAKTRQ.V...FYT.V
Retrocopy FIKTSAKTRQGVDNVFYTSV

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_520 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Dipodomys ordii	ENSDORG00000011469	1 retrocopy	retro_dord_520 ,
Erinaceus europaeus	ENSEEUG00000003058	1 retrocopy	retro_eeur_160,
Homo sapiens	ENSG00000133703	1 retrocopy	retro_hsap_3474,
Macaca mulatta	ENSMMUG00000015381	1 retrocopy	retro_mmul_1766,
Monodelphis domestica	ENSMODG00000017458	1 retrocopy	retro_mdom_153,
Nomascus leucogenys	ENSNLEG00000005266	1 retrocopy	retro_nleu_338,
Tupaia belangeri	ENSTBEG00000003830	2 retrocopies	retro_tbel_2242, retro_tbel_271,