RetrogeneDB ID: retro_dord_61

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1734:18888..19189(-)
• Located in intron of: ENSDORG00000001393

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cda
• Ensembl ID: ENSDORG00000011900
• Aliases: None
• Description: cytidine deaminase [Source:MGI Symbol;Acc:MGI:1919519]

Sequence

>retro_dord_61
GCCCTGGAGCCCGAGCACGTCCAGCGGCTTCTGCTGTCCTTCCCGCGAGGCCAAGAAGTCAGCCTACTGTCCCTACAGCC
ACTTCCCTGTGGGGGCCGCCCTGCTCACCCGCGATGGGAGGGTCTTCTCTGGATGCAACATAGAAAATGCTTGCTACCCT
CTGAGCTTGTGTGCTGAGCGGACTGCCATCCAGAAGGCCATCTCAGAAGGGCACAAGGATTTCAGGGCCATAGCTATCTC
CAGTGACCTGCAAGATGACTTCATCTCACCATGTGGAGGCTGTAGGCAAGTCATGAGAGAG

Alignment

ORF - retro_dord_61 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.02 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALEPEHVQRLLLS-SREAKKSAYCPYSHFPVGAALLTRDGRVFSGCNIENACYPLSVCAERTAIQKAISE
          ALEPEHVQRLLLS.SREAKKSAYCPYSHFPVGAALLTRDGRVFSGCNIENACYPLS.CAERTAIQKAISE
Retrocopy ALEPEHVQRLLLS>SREAKKSAYCPYSHFPVGAALLTRDGRVFSGCNIENACYPLSLCAERTAIQKAISE

Parental  GHKDFRAIAISSDLQDDFISPCGGCRQVMRE
          GHKDFRAIAISSDLQDDFISPCGGCRQVMRE
Retrocopy GHKDFRAIAISSDLQDDFISPCGGCRQVMRE

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_61 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011900	1 retrocopy	retro_dord_61 ,
Macropus eugenii	ENSMEUG00000016075	6 retrocopies	retro_meug_102, retro_meug_1601, retro_meug_1617, retro_meug_2041, retro_meug_527, retro_meug_603,
Ochotona princeps	ENSOPRG00000007364	2 retrocopies	retro_opri_282, retro_opri_603,