RetrogeneDB ID: retro_cfam_1273

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:7144787..7145693(-)
• Located in intron of: None

Retrocopy information

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

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_1273
ATGAAGCCATGGGGTGAGTGCAGGAGCTTCCTGGCTCCCGGCTTGCTGCAGCACCAGCTGGCCATCGTCACCGGCGGGGC
CACGGGCATCGGGAAGGCCATCGCCACCGAGCTCCTGCATCTGGGATGTAATTTGGTCATTGCATCTCGTAATTTTGATC
GATTAAAATCTACTGTAGATGAACTGAGGACCAGCCTACCCCTGACCAACCAGGCTCAGGTCACTCCCATAAAATGCAAC
ATTTGCAAAGAAGAGGTGAACAATTTGGTCAGATCCACCCTAGAGATTTATGGTAAAATCAACTTTTTGGTAAACAATGG
AGGAGGCCAGTTCATGGCTTCTATGGAAAACATTAATGCAAAGGGATGGCATGCTGTGGTTGAAACCAACCTGACAGGCA
CCTTCTACATGTGCAAACCAGTTTACAACTCCTGGATGAAAGAGCATGGAGGATCTATTGTCAATATTATTATCCTTACT
AGAAATGGATATCCAGGATTTACGCATAGTGGAGCTGCCAGAGCGGGGGTTTACAAGCTCACCAAATCCATAGCTGTGGA
ATGGGCCAACAGTGGAATAAGGATCAATTGTGTTGCCACTGGAACCATTTATTCCCCGAGTGCTGTTGACAACTATGGTC
CTTTGGCAGAAGACGTATTTGCAGGGTACTTTGAGAAAATCCCAGCTAAGTGAATTAGAGTGCCTGAGGAGATCTCCTTG
GTGGTCTGCTTCCTGCTGTCCCCTGCAGCTTCCTTCATCACTGGACAGTTGGTGAACGTGGACGGGGGCCAGTCTCTGTA
TACGCACATATTTGATGTACCAGATCATGACAACTGGCCTGATGGAGCAGGGGACATTTCCTTTGTCAAACATTTGAAGA
ATACTTTCAAGAGTAAAAGCAAGCTC

Alignment

ORF - retro_cfam_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPWVERRSFLAPDLLLHQLAIVTGGATGIGKAIATELLHLGCNVVIASRNFDRLKSTAEELRASLPPTN
          M.PW.E.RSFLAP.LL.HQLAIVTGGATGIGKAIATELLHLGCN.VIASRNFDRLKST..ELR.SLP.TN
Retrocopy MKPWGECRSFLAPGLLQHQLAIVTGGATGIGKAIATELLHLGCNLVIASRNFDRLKSTVDELRTSLPLTN

Parental  KAQVTPIKCNIRKEEEVNNLVRSTLEIYGKINFLVNNGGGQFMAAMEHINAKGWHAVIETNLTGTFYMCK
          .AQVTPIKCNI.KEE.VNNLVRSTLEIYGKINFLVNNGGGQFMA.ME.INAKGWHAV.ETNLTGTFYMCK
Retrocopy QAQVTPIKCNICKEE-VNNLVRSTLEIYGKINFLVNNGGGQFMASMENINAKGWHAVVETNLTGTFYMCK

Parental  AVYNSWMKEHGGSIVNIIILTRNGYPGFTHSGAARAGVYNLTKSLAVEWASSGIRINCVAPGTIYSPSAV
          .VYNSWMKEHGGSIVNIIILTRNGYPGFTHSGAARAGVY.LTKS.AVEWA.SGIRINCVA.GTIYSPSAV
Retrocopy PVYNSWMKEHGGSIVNIIILTRNGYPGFTHSGAARAGVYKLTKSIAVEWANSGIRINCVATGTIYSPSAV

Parental  DNYGPLAENMFAGYFEKIPAKRIGVPEEISSVVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW
          DNYGPLAE..FAGYFEKIPAK.I.VPEEIS.VVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW
Retrocopy DNYGPLAEDVFAGYFEKIPAK*IRVPEEISLVVCFLLSPAASFITGQLVNVDGGQSLYTHIFDVPDHDNW

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	0.00 RPM	8.36 RPM
SRP017611_brain	0.00 RPM	5.95 RPM
SRP017611_kidney	0.07 RPM	85.72 RPM
SRP017611_liver	0.00 RPM	54.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1273 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1273 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,