RetrogeneDB ID: retro_dord_264

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6822:223164..223453(+)
• Located in intron of: ENSDORG00000012056

Retrocopy information

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

Parental gene information

• Parental gene symbol: Polr2i
• Ensembl ID: ENSDORG00000001852
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide I [Source:MGI Symbol;Acc:MGI:1917170]

Sequence

>retro_dord_264
GGCTTTGTAGGTATTCACTTCTGCCAGGAATGTAACAACATGCTGTACCCCAAGGAAGACAAGGAGAACCACATCCTGCT
GTGCGTGTGCCAGAACTGTGACTACCAGCAGGAAGCAGACAGCAGTTACATCTAACGTCAACAAAATCAAGCACGAAGTG
GACAAACTGACCCAGATCATCGCGGACGTGTCCCAGGACCCCACTTTGCCTTGGACCGAAGACCACCCATGCCAGAAGTG
TGGCCACAAGGAGGCAGTGTTCTTCCAGTCACACAGTGTCTGGACTGAG

Alignment

ORF - retro_dord_264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 91.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCI-YVNKITHEVDELTQIIADVSQDPTL
          GFVGI.FCQECNNMLYPKEDKEN.ILL..C.NCDYQQEAD.S.I..VNKI.HEVD.LTQIIADVSQDPTL
Retrocopy GFVGIHFCQECNNMLYPKEDKENHILLCVCQNCDYQQEADSSYI>NVNKIKHEVDKLTQIIADVSQDPTL

Parental  PRTEDHPCQKCGHKEAVFFQSHSARAE
          P.TEDHPCQKCGHKEAVFFQSHS...E
Retrocopy PWTEDHPCQKCGHKEAVFFQSHSVWTE

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_264 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006601	1 retrocopy	retro_cfam_1400,
Callithrix jacchus	ENSCJAG00000009671	1 retrocopy	retro_cjac_2777,
Dipodomys ordii	ENSDORG00000001852	2 retrocopies	retro_dord_264 , retro_dord_555,
Monodelphis domestica	ENSMODG00000014172	1 retrocopy	retro_mdom_1465,
Mus musculus	ENSMUSG00000019738	1 retrocopy	retro_mmus_2287,
Oryctolagus cuniculus	ENSOCUG00000013044	2 retrocopies	retro_ocun_103, retro_ocun_1603,
Otolemur garnettii	ENSOGAG00000024254	1 retrocopy	retro_ogar_386,
Ochotona princeps	ENSOPRG00000001789	2 retrocopies	retro_opri_350, retro_opri_837,
Tursiops truncatus	ENSTTRG00000003919	1 retrocopy	retro_ttru_223,