RetrogeneDB ID: retro_cfam_1702

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:50355377..50355809(-)
• Located in intron of: ENSCAFG00000029901

Retrocopy information

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

Parental gene information

• Parental gene symbol: SURF2
• Ensembl ID: ENSCAFG00000019763
• Aliases: None
• Description: surfeit 2 [Source:HGNC Symbol;Acc:11475]

Sequence

>retro_cfam_1702
ATCTGTGCGTGAATACGGTGTCAGAAGCAGTATGTGGAGTGCGTGCCTGCCTGCCTCCTGCACAAAAGGAGGAGGAGGGA
AGACCAGTTGGACAGCACCGGCTGCCTCCCCCAAGAGAAGCCTCCTGGGAACCCGCTTCCAACAAAGATGGCACAGCTGC
GAGTGGCAGTGACGACAGCATGACAGATCTGTACCCACCCGAGTTGTTTACCAGAAACGATCTGGGAAGGACTGAGCATG
GGGATAGCACCGATGACTCTGGCAGAGGAGGAGGGTGAGAAGCCAAGGTGCCCCAGACAGAAGGGCCCTGGGGCCAGAGA
AGAGATGGAGGTGGACCCTGAGCAGGTCTTCAAGCATTGGGAGAAGCCGTTGGGCTCATCAAAGAAGTTCAAAAGTCGTC
ACCATAAACCTAAGAGCTTCAGCTCTTTTAAG

Alignment

ORF - retro_cfam_1702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.19 %
• Parental protein coverage: 56.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LCEYEKCQKQGVEYVPACLLHKRRRKEAQMDGTGP-PHSREAFWEPASSEDDAAASDSEDSMTDLYPPEL
          .C....CQKQ.VE.VPACLLHKRRR.E.Q.D.TG..P..REA.WEPAS..D..AAS.S.DSMTDLYPPEL
Retrocopy ICA*IRCQKQYVECVPACLLHKRRRREDQLDSTGC<PPPREASWEPASNKDGTAASGSDDSMTDLYPPEL

Parental  FTRKDLGRTEPGDSSSD-FLTEDEDGKPRLTPGKGPGDREEMEVAQALVHKRGKKQLSLSKKKFKSHHRK
          FTR.DLGRTE.GD.S.D..L.E.E..KPR....KGPG.REEMEV....V.K...K.L..S.KKFKS.H.K
Retrocopy FTRNDLGRTEHGD-STD>TLAEEEGEKPRCPRQKGPGAREEMEVDPEQVFKHWEKPLG-SSKKFKSRHHK

Parental  AKSFSSLK
          .KSFSS.K
Retrocopy PKSFSSFK

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	11.21 RPM
SRP017611_brain	0.00 RPM	11.11 RPM
SRP017611_kidney	0.00 RPM	9.31 RPM
SRP017611_liver	0.00 RPM	6.67 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1702 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1702 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019763	1 retrocopy	retro_cfam_1702 ,
Callithrix jacchus	ENSCJAG00000009532	5 retrocopies	retro_cjac_3362, retro_cjac_3452, retro_cjac_3606, retro_cjac_3648, retro_cjac_3914,
Felis catus	ENSFCAG00000028927	1 retrocopy	retro_fcat_277,
Monodelphis domestica	ENSMODG00000012766	1 retrocopy	retro_mdom_1894,