RetrogeneDB ID: retro_cfam_568

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:18208763..18209672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000835
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PECR
• Ensembl ID: ENSCAFG00000014368
• Aliases: None
• Description: Canis lupus familiaris peroxisomal trans-2-enoyl-CoA reductase (PECR), mRNA. [Source:RefSeq mRNA;Acc:NM_001252139]

Sequence

>retro_cfam_568
ATGAGGTCGTGGGTCGAGCGCAGGAGCTTCCTGGCTCCCGGCTTGCTGCTGCACCAGCTGGCCATCGTCACCGGCGGGGC
CACGGGCATCGGGAAGGCCATCGCCACCGAGCTCCTGCATCTGGGATGTAATGTGGTCATTGCATCTCGTAATTTTGATC
GATTAAAATCTACTGCAGAAGAACTGAGGGCCAGCCTACCCCCGACCAACCAGGCTCAGGTCACTCCCATAAAATGCAAC
ATTCGCAAAGAAGAAGAGGTGAACAATTTGGTCAGATCCACCTTAGAGATTTATGGTAAAATCAATTTTTTGGTAAACAA
TGGAGGAGGCCAGTTCGTGGCTGCTATGGAACACATTAATGCAAAGGGATGGCATGCTGTGATTGAAATCAACCTGACAG
GCACCTTCTACATGTGCAAAGCAGTTTACAATTCCTGGATGAAAGAGCCTGGAGGATCTATTGTCAATATTATTATCCTT
ACTAGAAATGGATATCCAGGATTTACGCATAGTGGAGCTGCCAGAGCAGGGGTTTACAACCTCACCAAATCCTTAGCTGT
GGAATGGGCCAGCAGTGGAATAAGGATCAACTGTGTTGCCCCTGGAACCATTTATTCCCCGAGTGCTGTTGACAACTATG
GTCCTTTGGCAGAAAACATGTTTGCAGGGTACTTTGGGAAAATCCCAGCTAAGCGAATTGGAGTGCCTGAGGAGATCTCC
TCGGTGGTCTGCTTCCTGCTGTCTCCTGCAGCTTCCTTCATCACTGGACAGTTGGTGAACGTGGACGGGGGCCAGTCTCT
GTATACGCACATATTCGACGTACCAGATCATGACAACTGGCCTGATGGAGCAGGGGACATTTCCTTTGTCAAACATTTGA
AGAATACTTTCAAGAGTAAAAGCAAGCTC

Alignment

ORF - retro_cfam_568 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPWVERRSFLAPDLLLHQLAIVTGGATGIGKAIATELLHLGCNVVIASRNFDRLKSTAEELRASLPPTN
          MR.WVERRSFLAP.LLLHQLAIVTGGATGIGKAIATELLHLGCNVVIASRNFDRLKSTAEELRASLPPTN
Retrocopy MRSWVERRSFLAPGLLLHQLAIVTGGATGIGKAIATELLHLGCNVVIASRNFDRLKSTAEELRASLPPTN

Parental  KAQVTPIKCNIRKEEEVNNLVRSTLEIYGKINFLVNNGGGQFMAAMEHINAKGWHAVIETNLTGTFYMCK
          .AQVTPIKCNIRKEEEVNNLVRSTLEIYGKINFLVNNGGGQF.AAMEHINAKGWHAVIE.NLTGTFYMCK
Retrocopy QAQVTPIKCNIRKEEEVNNLVRSTLEIYGKINFLVNNGGGQFVAAMEHINAKGWHAVIEINLTGTFYMCK

Parental  AVYNSWMKEHGGSIVNIIILTRNGYPGFTHSGAARAGVYNLTKSLAVEWASSGIRINCVAPGTIYSPSAV
          AVYNSWMKE.GGSIVNIIILTRNGYPGFTHSGAARAGVYNLTKSLAVEWASSGIRINCVAPGTIYSPSAV
Retrocopy AVYNSWMKEPGGSIVNIIILTRNGYPGFTHSGAARAGVYNLTKSLAVEWASSGIRINCVAPGTIYSPSAV

Parental  DNYGPLAENMFAGYFEKIPAKRIGVPEEISSVVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW
          DNYGPLAENMFAGYF.KIPAKRIGVPEEISSVVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW
Retrocopy DNYGPLAENMFAGYFGKIPAKRIGVPEEISSVVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW

Parental  PDGAGDVSFVKHLKNTFKSKSKL
          PDGAGD.SFVKHLKNTFKSKSKL
Retrocopy PDGAGDISFVKHLKNTFKSKSKL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.04 RPM	8.36 RPM
SRP017611_brain	0.32 RPM	5.95 RPM
SRP017611_kidney	1.92 RPM	85.72 RPM
SRP017611_liver	5.44 RPM	54.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_568 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005927	1 retrocopy	retro_cfam_2172,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341,
Canis familiaris	ENSCAFG00000014368	4 retrocopies	retro_cfam_1199, retro_cfam_1212, retro_cfam_1273, retro_cfam_568 ,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Sarcophilus harrisii	ENSSHAG00000001503	1 retrocopy	retro_shar_708,