RetrogeneDB ID: retro_cfam_555

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:47983176..47983845(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSI1
• Ensembl ID: ENSCAFG00000010283
• Aliases: None
• Description: musashi RNA-binding protein 1 [Source:HGNC Symbol;Acc:7330]

Sequence

>retro_cfam_555
AAAATGTTTATCGGCGGACTAAGCTGGCAGACCTCACCAGATAGCCTTAGAGACTATTTTAGCAAATTTGGAGAAATTAG
AGAATGTATGGTCATGAGAGATCCCACTACGAAACGCTCCAGAGGCTTCGGTTTCGTCACGTTCGCAGATCCAGCAAGTG
TAGATAAAGTATTAGGTCAGCCCCACCATGAGTTAGATTCCAAGACGATTGATCCTAAAGTTGCATTTCCTCGTCGGGCA
CAACCCAAGATGGTCACAAGAACAAAGAAAATATTTGTAGGCGGATTATCTGCGAACACAGTGGTGGAAGATGTAAAGCA
ATACTTTGAGCAGTTTGGCAAGGTGGAGGACGCAATGCTGATGTTTGATAAGACAACCAACAGGCACAGAGGGTTTGGCT
TTGTCACGTTTGAGAATGAAGATGTTGTGGAGAAAGTCTGTGAGATTCATTTCCATGAAATCAATAATAAAATGGTAGAA
TGTAAGAAAGCTCAGCCTAAGGAAGTCATGTTCCCACCGGGGACAAGAGGCCGGGCCCGGGGACTGCCTTATACCATGGA
CGCGTTCATGCTTGGCATGGGAATGCTAGGCTACCCCAACTTTGTGGCAACCTATGGCCGCGGCTACCCTGGATTTGCTC
CTAGCTATGGTTATCAGTTCCCAGACTAC

Alignment

ORF - retro_cfam_555 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 62.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI
          KMFIGGLSWQT....LR.YF..FGE..EC.VMRDP.TKRSRGFGFVTF.D.A.VDKVL.Q..HELDSKTI
Retrocopy KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLGQPHHELDSKTI

Parental  DPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKQYFEQFEKVDDAMLMFDKTTNRHRGFGFVTFESE
          DPKVAFPRRAQPKMVTRTKKIFVGGLS.NT.VEDVKQYFEQF.KV.DAMLMFDKTTNRHRGFGFVTFE.E
Retrocopy DPKVAFPRRAQPKMVTRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENE

Parental  DIVEKVCEIHFHEINNKMVECKKAQPKEVMSPTGSARGRSRVMPYGMDAFMLGIGMLGYPGFQATTYASR
          D.VEKVCEIHFHEINNKMVECKKAQPKEVM.P.G..RGR.R..PY.MDAFMLG.GMLGYP.F.AT....R
Retrocopy DVVEKVCEIHFHEINNKMVECKKAQPKEVMFPPGT-RGRARGLPYTMDAFMLGMGMLGYPNFVAT--YGR

Parental  SYTGLAPGYTYQFPEF
          .Y.G.AP.Y.YQFP..
Retrocopy GYPGFAPSYGYQFPDY

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	18.90 RPM	56.78 RPM
SRP017611_brain	7.30 RPM	7.94 RPM
SRP017611_kidney	14.59 RPM	3.37 RPM
SRP017611_liver	2.32 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_555 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_555 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010283	1 retrocopy	retro_cfam_555 ,
Ictidomys tridecemlineatus	ENSSTOG00000009799	1 retrocopy	retro_itri_779,