RetrogeneDB ID: retro_ecab_623

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:46266288..46266626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLDN1
• Ensembl ID: ENSECAG00000021074
• Aliases: None
• Description: claudin 1 [Source:HGNC Symbol;Acc:2032]

Sequence

>retro_ecab_623
GCCACCATTGCCATGAAAAGTCTAAAGTGCTTGGAGGATGCTGAGATGTAGAAGAGGTGAATGGCTATCATTGGAGTTTT
GTTTTTATTGTTGTAGATCTGGCTATTTTAGTTGCCACAGCATAGTAAGACGATAAAATTGTGCAAGAGGTTTATCAGTC
AATGACCCCAGTCAATGCCAGGGATGAATGGGTCAAGCTCTCTTTAATGTCTTGGCTACTGCTCTCACTGCCTTCTGAGA
AGTGCCCTATTTTGCTTTCCTGACTCCCCCAAAAGACCTCTTACCTAACACCACTGCCCTATCCTAAACCCATACCTTCT
AATGGAAAGTACCACATA

Alignment

ORF - retro_ecab_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.54 %
• Parental protein coverage: 54.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ATVGMKCMKCMEDDEVQKMRMAVIG-GVIFLFAGLAVLVATAWYGNRIVQEFYDPMTPVNARYEF-GHAL
          AT..MK..KC.ED.E..K..MA.IG....F....LA.LVATA.....IVQE.Y..MTPVNAR.E..G.AL
Retrocopy ATIAMKSLKCLEDAEM*KR*MAIIG<SFVFIVVDLAILVATA**DDKIVQEVYQSMTPVNARDEW<GQAL

Parental  FTGWAAA-SLCLLGGGLLCCSCPRK-TTSYPTPRPYPKPAPSSGKDYV
          F...A.A.S.CLL...L.C.....K..TSY.TP.PYPKP.PS.GK...
Retrocopy FNVLATA<SHCLLRSALFCFPDSPK<KTSYLTPLPYPKPIPSNGKYHI

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	0.18 RPM
SRP021940_cerebellum	0.00 RPM	0.68 RPM
SRP021940_embryo	0.03 RPM	9.79 RPM
SRP021940_placental_villous	0.00 RPM	56.39 RPM
SRP021940_synovial_membrane	0.00 RPM	1.18 RPM
SRP021940_testis	0.00 RPM	0.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_623 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_623 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
Equus caballus	ENSECAG00000021074	1 retrocopy	retro_ecab_623 ,
Sus scrofa	ENSSSCG00000028484	1 retrocopy	retro_sscr_1006,