RetrogeneDB ID: retro_dord_560

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3236:64544..65168(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pafah1b2
• Ensembl ID: ENSDORG00000011274
• Aliases: None
• Description: platelet-activating factor acetylhydrolase, isoform 1b, subunit 2 [Source:MGI Symbol;Acc:MGI:108415]

Sequence

>retro_dord_560
ATGAGCCAAGGAGACTTGAACCCAGCAGCTATCCCACATGCAGCAGAAGATATTCAAGGTGATGACAGATGGATGTCTCA
GCACAATAGATTCGTCTTGGACTGTAAAGACAAAGAGCCTGATGTACTGTTTGTGGGAGACTCCGTGACACAGTTAATAC
AGCAGTATGAGATATGGCGAGAACTTTTTTCCCCACTTCATGCACTTAATTTTGGAATTGGAGGGGATACAACAAGACAT
GTTCTATGGAGACTAAAGAATGGAGGACTGGAGAACATTAAACCTAAGGTCATTGTTGTTTGGGTAGGAACAAACAACCA
ACCTGCAGAAGAAGTAGCAGGTGGAATTGAAGCCATTGTACAGCTCATCAACACCAGGCAGCCACAGGCCAAAATCATTG
TACTGGGTTTATTACCTCGAGGTGAGAAGCCCAACCCTTTGAGGCAAAAGAATGCCAAGGTGAACCAACTTCTCAAGGTT
TCACTGCCGAAGCTTGCTAATGTGCAGCTCCTGGATACAGATGGGGGCTTCGGTCACTCGGACGGTGCCATTTCCTGTCA
CGACATGTTTGATTTTCTGCATCTCACAGGAGGGGGCTATGCAAAGATCTGCAAGCCCCTCCAT

Alignment

ORF - retro_dord_560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMIQLMQQYEIWRELFSPLHALN
          MSQGD.NPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDS..QL.QQYEIWRELFSPLHALN
Retrocopy MSQGDLNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSVTQLIQQYEIWRELFSPLHALN

Parental  FGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIIVLGLL
          FGIGGDTTRHVLWRLKNG.LENIKPKVIVVWVGTNN....AEEVAGGIEAIVQLINTRQPQAKIIVLGLL
Retrocopy FGIGGDTTRHVLWRLKNGGLENIKPKVIVVWVGTNN--QPAEEVAGGIEAIVQLINTRQPQAKIIVLGLL

Parental  PRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPLH
          PRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDTDGGF.HSDGAISCHDMFDFLHLTGGGYAKICKPLH
Retrocopy PRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDTDGGFGHSDGAISCHDMFDFLHLTGGGYAKICKPLH

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_560 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560 ,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,