RetrogeneDB ID: retro_dord_575

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3514:81770..82073(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppil3
• Ensembl ID: ENSDORG00000007389
• Aliases: None
• Description: peptidylprolyl isomerase (cyclophilin)-like 3 [Source:MGI Symbol;Acc:MGI:1917475]

Sequence

>retro_dord_575
AGAGGAGGTAACAGTATCTGGGGCAAGAAGTTTGAGGATGAGTACAGTGAATATCTTAAGCACAATGTTAGAGGGGTTGT
ATCTATGGCAAATAATGGCCCAAACACCAATGGATCTCAGTTTTTCATCACCTATGGCAAGCAACCACATTTGGACATGA
AACATACAGTATTTGGAAAAGTGAGAGATGGTCTGGAGACTCTGGATGAGTTGGAGAAGTTACCAGTAAATGAAAAGACA
TACCGACCTCTTAATGATGTACACATTAAGGATATAACTACTCATGCCAACCCATTTGCTCAG

Alignment

ORF - retro_dord_575 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 61.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDE
          RGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMK.TVFGKV.DGLETLDE
Retrocopy RGGNSIWGKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKHTVFGKVRDGLETLDE

Parental  LEKLPVNEKTYRPLNDVHIKDITIHANPFAQ
          LEKLPVNEKTYRPLNDVHIKDIT.HANPFAQ
Retrocopy LEKLPVNEKTYRPLNDVHIKDITTHANPFAQ

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_575 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005917	1 retrocopy	retro_amel_1458,
Bos taurus	ENSBTAG00000005416	1 retrocopy	retro_btau_1585,
Canis familiaris	ENSCAFG00000032245	1 retrocopy	retro_cfam_180,
Dasypus novemcinctus	ENSDNOG00000002364	1 retrocopy	retro_dnov_2477,
Dipodomys ordii	ENSDORG00000007389	1 retrocopy	retro_dord_575 ,
Dipodomys ordii	ENSDORG00000016152	3 retrocopies	retro_dord_151, retro_dord_173, retro_dord_447,
Monodelphis domestica	ENSMODG00000015037	1 retrocopy	retro_mdom_1025,
Tupaia belangeri	ENSTBEG00000000664	1 retrocopy	retro_tbel_4520,