RetrogeneDB ID: retro_ecab_639

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:28121650..28122352(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSK
• Ensembl ID: ENSECAG00000013581
• Aliases: None
• Description: c-src tyrosine kinase [Source:HGNC Symbol;Acc:2444]

Sequence

>retro_ecab_639
CCCAAGACAGGCCTGTTCCTGGTGTGGGAGAGCATCAACTACCCTGGGGACTATACGCTGTCTGTGAACTGTGAAGGCAA
AGTGGAGCACTACAGCATCATGTACGACAACAGCAAGCTCAGCATTAGTGAGGAGGTGTACTTCGAGAGCCTCATGCAGC
TGGTGGAGCACTACACCTCAGGTGCAGATGAAATCTGTACTTGCCTCATCAAGCCAAAGGTCATGGAGGGCACAGAGGAG
GTCCAGGATGAGCTCTTCCTCAGAGGCTGGACGCTGAACATAAAGGACCTGAAGCTGCTGCAGATCACTGGGAAGGGGGA
CTTTGGAGACGTGATGCTGAGCTGTTGTGGAGGGAACAAAGTCTCTGTCAATTACGTTAGGAACGACACTACTGCCCAAG
CATTCCTGGCTGAAGCCTTGGTCATGGCACAAGTTCATCCTAGCAACCAGGTACAGCTTTTGGGCGTGATCACGGCGCAG
AAACGTGGCCTTTACATCATCACTGAGTTCATGGCCAAGGGGAGCCTGGTGGATTACCGGCAGTTGCTGGATTGGTAGGT
GCTGGGCAGAGACTTTCTCCTCAAATTCTCACTAGACCTCCGTGAGACCATGAAGTACCCAGAGAGCAACAACTTCGTAC
ACCGGGGCCTTGCTGCCGGCGCCATGCTGGTATCCGAGGACAGCGTGGCCAAGGTCAAGGAC

Alignment

ORF - retro_ecab_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.51 %
• Parental protein coverage: 52.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLI
          P.TGLFLV.ES.NYPGDYTL.V.C.GKVEHY.IMY..SKLSI.EEVYFE.LMQLVEHYTS.AD..CT.LI
Retrocopy PKTGLFLVWESINYPGDYTLSVNCEGKVEHYSIMYDNSKLSISEEVYFESLMQLVEHYTSGADEICTCLI

Parental  KPKVMEGTVAAQDEFFRSGWALNMKDLKLLQTIGKGEFGDVMLGDYRGNKVAVKCIKNDATAQAFLAEAS
          KPKVMEGT...QDE.F..GW.LN.KDLKLLQ..GKG.FGDVML....GNKV.V....ND.TAQAFLAEA.
Retrocopy KPKVMEGTEEVQDELFLRGWTLNIKDLKLLQITGKGDFGDVMLSCCGGNKVSVNYVRNDTTAQAFLAEAL

Parental  VMTQLRHSNLVQLLGVIVEEKGGLYIVTEYMAKGSLVDYLRSRGRSVLGGDCLLKFSLDVCEAMEYLEGN
          VM.Q...SN.VQLLGVI...K.GLYI.TE.MAKGSLVDY.......VLG.D.LLKFSLD..E.M.Y.E.N
Retrocopy VMAQVHPSNQVQLLGVITAQKRGLYIITEFMAKGSLVDYRQLLDW*VLGRDFLLKFSLDLRETMKYPESN

Parental  NFVHRDLAARNVLVSEDNVAKVSD
          NFVHR.LAA...LVSED.VAKV.D
Retrocopy NFVHRGLAAGAMLVSEDSVAKVKD

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
SRP021940_articular_cartilage	0.00 RPM	24.67 RPM
SRP021940_cerebellum	0.05 RPM	42.48 RPM
SRP021940_embryo	0.00 RPM	63.96 RPM
SRP021940_placental_villous	0.00 RPM	30.41 RPM
SRP021940_synovial_membrane	0.00 RPM	64.46 RPM
SRP021940_testis	0.00 RPM	25.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_639 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013581	1 retrocopy	retro_ecab_639 ,
Myotis lucifugus	ENSMLUG00000013625	1 retrocopy	retro_mluc_1162,
Sus scrofa	ENSSSCG00000001900	1 retrocopy	retro_sscr_953,