RetrogeneDB ID: retro_dord_704

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5888:41781..42390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Polr2c
• Ensembl ID: ENSDORG00000000081
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide C [Source:MGI Symbol;Acc:MGI:109299]

Sequence

>retro_dord_704
TACGCCAACCAGCCCACCGTGGGCATCACGGAGCTCACGGAAGAGAACGTCAAGTTCATCATCGAGAACACGGACCTGGC
GGTGGCCAATTCTATTGGAAGAGTCTTCATCCCCCAGGTACCCATAATAGCCATCGACTGGGTCCAGATTGATGCCAGTT
CTTCCATCTTCATGATGAGTTCATTGCTCACAGCTTGGACTAATTCCACTCACCGGTGATGACATCGTGGACAAGCTGCA
ATACTCTCGGGACTGTACACGTGAGGAGTTCTGCCCGAGTGCTCAGTGGAGTTCACTCTGGATGTGCGGTGTAATGAAGA
CCAGACACGTCACGTCACATCCCGAGACCTCATCTCCAACAGCCCCCGGGTCATTCCAGTGACATCCCGGAAGCGCGATA
ACGACCCCAATGACTACGTGGAGCAGGATGACATCCTCATCGTCAAGCTGAGGAAGGGCCAGGAGCTGAGACTTCGAGCC
TATGCCCAAAACGGCTTCTGCAAGGAACATGCCAAGTGGAACCCCACTGCAGGGGTGGCTTTTGAACATGACCCAGACGA
TGTCCCGAGGCACACAGATTACCCCAAACCTGAGGAATGGCCAAAGAGC

Alignment

ORF - retro_dord_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.37 %
• Parental protein coverage: 74.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSV-LHDEFIAH-RLGL
          YANQPTV.ITELT.ENVKFIIENTDLAVANSI.RVFI..VPIIAIDWVQIDA.SS..LHDEFIAH..LGL
Retrocopy YANQPTVGITELTEENVKFIIENTDLAVANSIGRVFIPQVPIIAIDWVQIDASSSI<LHDEFIAH<QLGL

Parental  IPLTSDDIVDKLQYSRDCTCEEFC-PECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDP
          IPLT.DDIVDKLQYSRDCT.EEFC.PECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSR.RDNDP
Retrocopy IPLTGDDIVDKLQYSRDCTREEFC<PECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRKRDNDP

Parental  NDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKS
          NDYVEQDDILIVKLRKGQELRLRAYA..GF.KEHAKWNPTAGVAFE.DPD...RHT.YPKPEEWPKS
Retrocopy NDYVEQDDILIVKLRKGQELRLRAYAQNGFCKEHAKWNPTAGVAFEHDPDDVPRHTDYPKPEEWPKS

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_704 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008720	1 retrocopy	retro_cfam_688,
Choloepus hoffmanni	ENSCHOG00000002986	1 retrocopy	retro_chof_1988,
Callithrix jacchus	ENSCJAG00000012016	1 retrocopy	retro_cjac_2026,
Dipodomys ordii	ENSDORG00000000081	1 retrocopy	retro_dord_704 ,
Echinops telfairi	ENSETEG00000004185	1 retrocopy	retro_etel_1953,
Homo sapiens	ENSG00000102978	1 retrocopy	retro_hsap_2496,
Gorilla gorilla	ENSGGOG00000012415	1 retrocopy	retro_ggor_1557,
Myotis lucifugus	ENSMLUG00000015833	2 retrocopies	retro_mluc_129, retro_mluc_236,
Macaca mulatta	ENSMMUG00000020474	1 retrocopy	retro_mmul_1674,
Mus musculus	ENSMUSG00000031783	1 retrocopy	retro_mmus_1723,
Nomascus leucogenys	ENSNLEG00000003034	1 retrocopy	retro_nleu_1431,
Otolemur garnettii	ENSOGAG00000016866	1 retrocopy	retro_ogar_3361,
Ochotona princeps	ENSOPRG00000006979	1 retrocopy	retro_opri_445,
Pongo abelii	ENSPPYG00000007390	1 retrocopy	retro_pabe_1839,
Pan troglodytes	ENSPTRG00000008157	1 retrocopy	retro_ptro_1448,