RetrogeneDB ID: retro_cfam_546

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:26999135..26999753(+)
• Located in intron of: ENSCAFG00000001093

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSCAFG00000018538
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_cfam_546
ATGCCTGGGCACTTACAGGAAGGCTTCAGCTGCGTGGTCACCAACCGATTCGACCAGTTATTTGACGACGAATCGGACCC
CTTTGAGGTGTTGAAGGCAGCAGAGAACAAGAAAAAAGAAGCCGGCAGGGGCAGTGTTGGGGGCCCTGGGGCCAAGAGCA
CAGCTCAGGCCGCAGCCCAGACCAACTCCAACGCGGCAGGCAAACAGCTGCGTAAAGAGTCCCAGAAAGACCACAAGAAC
CCGCTGCCCCCCAACGTTGGCGTGGCTGACAAGAAAGAGGAGACGCAGCCGCCCGTGGCGCTTAAGAAAGAAGGAATAAG
ACGTGTTGGAAGAAGACCTGATTAACAACTGCAGAGTGAAGGGAAAATAATTGATAGGAGACCAGAAAGGGGACCACCTC
GTGAACGACGATTTGAAAAGCCACTTGAAGAAAAGGGTGAAGGAGGAGAATTTTCAGTTGATAGACCGATTATTGACCGG
CCTATTCGAGGCCGTGGTGGTCTTGGAAGAGGTTGAGGAGGCCGCGGACGTGGAATGGGCCGAGGAGATGGATTTGATTC
TCGTGGCAAACGTGAATTTGATAGGCATAGTGGAAGTGATTGATCTGGCCAGAAGCAT

Alignment

ORF - retro_cfam_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.72 %
• Parental protein coverage: 50.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSSAAGKQL
          MPGHLQEGF.CVVTNRFDQLFDDESDPFEVLKAAENKKKEAG.G.VGGPGAKS.AQAAAQTNS.AAGKQL
Retrocopy MPGHLQEGFSCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGRGSVGGPGAKSTAQAAAQTNSNAAGKQL

Parental  RKESQKDRKNPLPPSVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQSEGKIIDRRPERRPPRERRFEK
          RKESQKD.KNPLPP.VGV.DKKEETQPPVALKKEGIRRVGRRPD.QLQSEGKIIDRRPER.PPRERRFEK
Retrocopy RKESQKDHKNPLPPNVGVADKKEETQPPVALKKEGIRRVGRRPD*QLQSEGKIIDRRPERGPPRERRFEK

Parental  PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSH
          PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRG.GGRGRGMGRGDGFDSRGKREFDRHSGSD.S...H
Retrocopy PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRG*GGRGRGMGRGDGFDSRGKREFDRHSGSD*SGQKH

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	0.59 RPM	220.91 RPM
SRP017611_brain	0.64 RPM	122.03 RPM
SRP017611_kidney	2.31 RPM	195.54 RPM
SRP017611_liver	0.94 RPM	104.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_546 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_546 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018538	1 retrocopy	retro_cfam_546 ,
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Homo sapiens	ENSG00000142864	3 retrocopies	retro_hsap_3056, retro_hsap_413, retro_hsap_4695,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Otolemur garnettii	ENSOGAG00000025884	1 retrocopy	retro_ogar_185,
Pan troglodytes	ENSPTRG00000023560	2 retrocopies	retro_ptro_1985, retro_ptro_317,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,