RetrogeneDB ID: retro_ecab_528

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:112845580..112846199(-)
• Located in intron of: ENSECAG00000024339

Retrocopy information

• Ensembl ID: ENSECAG00000024427
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000019846
• Aliases: None
• Description: None

Sequence

>retro_ecab_528
AACAGCAGAGCAGATGATACAAAAGAATGAATCAGTGAGTTGGACAAAAGAGCAGAGGAAATCACCAAAGCCAAACAGAA
AAAAGAAAAAATAATGAAAAAGAATGAGAACAGTATAAGGGACTTCTGGGACAACATCAAGCATAGTAACATCCACCTTA
TAGGTGTCCCAGAAGGTGAAGAGGAAGACAAAGGGGCTGAAAAATTATTTGAATAATAGCTGAAAACTTCCCTAACCAGG
AGAAGGAAACAGACATCCAGGTACAGGAAGCACAGAGAGTACCAAACAAGAGGAACCCAAAGAGGCCCACACCAAGACAC
ATTATAATTAAAATGTAAAGAATTAAAGTTAAAGAGAGAATCCTAAAAGCTGCAAGAGAAAAGCAACAAATTACATACAA
AGGAAATTCCATAAGGCTATCAGCTGACTTTTCAGCAAAAACTTCACAGGCTAGAAGGGAGGCACGATATATTCAAAGTG
CTGAAAGGAAAAAATCTGCAACCAAGAATACCCAGCAAGGTTATCATTCAGAATGGAAAGAGATAAAGAGCTTTCCAAAT
AGCAAAAACTAAAGGGGTTCATCACCACTAAACTGGTATTATAAGCAATGTTAAAGGGG

Alignment

ORF - retro_ecab_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.02 %
• Parental protein coverage: 92.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVIGVP--EERQRGRKLFE
          NSR.....E.I..LD...................NENS.R..WDNIK..NIH.IGVP..EE...G.....
Retrocopy NSRADDTKE*ISELDXXXXXXXXXXXXXXXXXXXNENSIRDFWDNIKHSNIHLIGVPEGEEEDKGAEKLF

Parental  E-IIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAARERQQVTYKGKPIR
          E.IIAE.FPN..KETD.QVQEAQRVPNK..PKRPT.RHIIIKM..IK.KERILKAARE.QQ.TYKG..IR
Retrocopy E<IIAENFPNQEKETDIQVQEAQRVPNKRNPKRPTPRHIIIKM*RIKVKERILKAAREKQQITYKGNSIR

Parental  LSVDFSAKTLQVRREWHDIFK-VKEKNLQPRILYPAR-LSFTMEGEIKSFQDKQKLKEFITKKPILQEML
          LS.DFSAKT.Q.RRE...I....K.KNLQPRI..P...LSF.ME...K.....QKLK.FIT.K..L..ML
Retrocopy LSADFSAKTSQARREARYIQS>LKGKNLQPRI--PSK>LSFRMERD-KELSK*QKLKGFITTKLVL*AML

Parental  KG
          KG
Retrocopy KG

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_528 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019846	8 retrocopies	retro_ecab_1033, retro_ecab_391, retro_ecab_528 , retro_ecab_531, retro_ecab_540, retro_ecab_574, retro_ecab_615, retro_ecab_918,