RetrogeneDB ID: retro_cfam_1212

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:31245077..31245684(-)
• 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_1212
CACCAGGCTCAGGTCACTCCCATAAAATGCAACATCTGCAAAGAAAAGGCGGTGAACAATTTGGTCAAATCCACCTTAGA
TATTTATGGTAAGATCAATTTTTTGTAAACAATGGAGGAGGTCAGTTCAGGTCTCCTGCAAAACACATCAGTGCAAAGGG
ATGGCATGCTGTGATCGAAACCAAATTGATGAGCACCTTCTACATGTGGAGAGCAGTTTACAACTCCTGGATGAAAGAGC
ATGGAGGATCCATTCTGAATAATATTATCCTTGTTTAAAATGGATTTCCAGGACTTGTGTATAGTGCAGCTGCCAGAGCA
GGTGTTTACAATCTCACCAAATCCTTGGCTGTAGAATAGGCCAGAACGGAGTAAGGAGCAACTGTGTTGCCCCTGGCGTC
ATTTATTCCCTGACTGCTATTGACAACTATGGCTCTTTGGCAAAAGACGTATTTGGACGGTTAAGAAAATTCCAGCGAAG
CAAATTGGAGTTCCTGAGAGATCTCCCTATTGGTCTGCTTCCTGCTGTCTCCTGTAGCTTCTCTTATCACTGGAAAATTG
GTGGATGGGGATGGGGCCAGTCTTTGTATATGGGAGTATTTGATATA

Alignment

ORF - retro_cfam_1212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.95 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NKAQVTPIKCNIRKEEEVNNLVRSTLEIYGKINFL-VNNGGGQFMAAMEHINAKGWHAVIETNLTGTFYM
          ..AQVTPIKCNI.KE..VNNLV.STL.IYGKINFL.VNNGGGQF.....HI.AKGWHAVIET.L..TFYM
Retrocopy HQAQVTPIKCNICKEKAVNNLVKSTLDIYGKINFL<VNNGGGQFRSPAKHISAKGWHAVIETKLMSTFYM

Parental  CKAVYNSWMKEHGGSIVNIIILTRNGYPGFTHSGAARAGVYNLTKSLAVEWA-SSGIRINCVAPGTIYSP
          ..AVYNSWMKEHGGSI.N.IIL..NG.PG...S.AARAGVYNLTKSLAVE.A...G.R.NCVAPG.IYS.
Retrocopy WRAVYNSWMKEHGGSILNNIILV*NGFPGLVYSAAARAGVYNLTKSLAVE*A<QNGVRSNCVAPGVIYSL

Parental  SAVDNYGPLAENMFAGYFEK-IPAKRIGVPE-EISSVVCFLLSPAASFITGQLVNVDG-GQSLYTHIFDV
          .A.DNYG.LA...F.G...K.IPAK.IGVPE.EIS..VCFLLSP.AS.ITG.LV..DG.GQSLY...FD.
Retrocopy TAIDNYGSLAKDVF-GRLRK<IPAKQIGVPE<EISLLVCFLLSPVASLITGKLVDGDG<GQSLYMGVFDI

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	0.00 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_1212 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1212 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1212 has 0 orthologous retrocopies within eutheria group .

---

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,