RetrogeneDB ID: retro_cfam_1093

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:2149182..2150072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000023585
• Aliases: None
• Description: None

Sequence

>retro_cfam_1093
ATGCTAAGCATTAAATAATCAGCCATATTACAGCAGAATGTGGCTGATTATTCAAAAGTGAATGAAGAGAACCATGAGTG
ATACCAATATACTCAGGTGATGCCAGCAGCAGGGACACTCAGAAAGCAGGGCACTTTTATCAAGTGGTTCAGAAAGAAGG
TGATTGAGAGAGGCCTTCGGACAGTGTTATAGTTTCTATCAACAAAGGACACGGGGAATATGCAGCACTCATAGGTCATC
AGTGGCAGGATCATGGCTTTGTGGTGGAAATGGCTCACCTCCCTGCCAAGTTGAGTCTTGCACAAGCACCCTAGAAAGTT
AAAGATGATGGGTCCCCATTTTGCATTCTTGTTGAACAGTCTAATGTAAAACTTTCTTCTTGTACCACAATTATGCTTCA
TGGGTCTATCAAAATGCATCTTATATTCCCCTGGACAATGCCTTAGCTAAAGAATACAGAAGATTTTTCTCTAAACAGGA
GCAGCAGCAATGTGCTGAATTGCTCTTTAGCCATGAGATCTGGTGGAGGACTTCTTGGCTTGGGAGTGGCTTGGCTTGGG
CCTCATCAGTTATTCTGTGCCTTCTGGCATTCAGTACCTTCTCTTCCTGTTGACTGAGAGAAAGCATTTGTACAGGAGTG
ATTTGAACTTCTCATTGACCACCAGAAGACCAGGAAAGGGTAACTAGAAGGCTTGGAGACCCTGGAGTCTTTGACTAGCA
ATGATCACTCCTCATTTCAAGGCAGGAATACACCCATTGTGGGCAAGCCACCTCCACTTCTTCCAACCTCTGGAAAGTGA
TTCTTCTAAGGTCTTCATTCCCCCCTTCCTGCCATGTTCCCATTGTTAGGAGACAGACCAGGAGGAGCTCTCCTTCCACA
ACAGGATTGG

Alignment

ORF - retro_cfam_1093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.31 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLSIK---ELWRNVADYSKRNEENHERPQTTQL-DDASIRDTRKEGLFQHFYQVVQKERDRERPSDCVIV
          MLSIK....L..NVADYSK.NEENHE..Q.TQ..D..S.RDT.K.G...HFYQVVQKE.D.ERPSD.VIV
Retrocopy MLSIK*SAILQQNVADYSKVNEENHE*YQYTQV<DASS-RDTQKAG---HFYQVVQKEGD*ERPSDSVIV

Parental  YINNEQREYATGIGHRLQDHDLVVEMIHLSSESSLMRALQEVKDDGSPFCILVEQSNVKLSSCTVIMLHE
          .IN....EYA..IGH..QDH..VVEM.HL....SL..A...VKDDGSPFCILVEQSNVKLSSCT.IMLH.
Retrocopy SINKGHGEYAALIGHQWQDHGFVVEMAHLPAKLSLAQAP*KVKDDGSPFCILVEQSNVKLSSCTTIMLHG

Parental  SIKIH-RHMPLEDALVLVAKEYRRFFSKREQQERTR-VALRAGDLVDDFLARERL----TSYSVPSDIQH
          SIK.H....PL..AL...AKEYRRFFSK.EQQ......AL...DLV.DFLA.E.L.....SYSVPS.IQ.
Retrocopy SIKMH<SYIPLDNAL---AKEYRRFFSKQEQQQCAE<IAL*P*DLVEDFLAWEWLGLGLISYSVPSGIQY

Parental  LLFLLTEGKHLYGNELN-LLIDYLTTRKGQLEGFETPESLASN-HSSFQGRNTPVVGKLPPLLPTPGKQS
          LLFLLTE.KHLY...LN.LLID...TRKG.LEG.ET.ESL.SN.HSSFQGRNTP.VGK.PPLLPT.GK..
Retrocopy LLFLLTERKHLYRSDLN<LLIDHQKTRKG*LEGLETLESLTSNDHSSFQGRNTPIVGKPPPLLPTSGK*F

Parental  FPGSHLPLPAKSPLLGDRPGGALLPPPDW
          F.G.H.PLPA..PLLGDRPGGALLP..DW
Retrocopy F*GLHSPLPAMFPLLGDRPGGALLPQQDW

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	3.19 RPM
SRP017611_brain	0.00 RPM	0.32 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	1.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1093 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023585	1 retrocopy	retro_cfam_1093 ,
Felis catus	ENSFCAG00000031110	1 retrocopy	retro_fcat_1384,