RetrogeneDB ID: retro_ecab_934

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:66274912..66275602(+)
• Located in intron of: ENSECAG00000021733

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000005242
• Aliases: None
• Description: None

Sequence

>retro_ecab_934
AATAAGAATTTGAACAAAGAGAGAGAAAATATAACAAAGCACCAAACAGAAATCACAGAGCTAAGAAATACAGTAACGGA
ACTGAAAAATACAGTAGAGGGGTTCAAAAGCAGATTAGATGAAGCAGAAGAAAGGATCACCAAACTCAAAGACAGGGCGG
TGGAATTCATCCAATCAGAACAACAAAAAGAAAAAAGAATGAAAAAGAGTGAAAACAGCTTAAGGGACTTAAGGCACAAT
ATCAAATGGACTAATATTCACCATATAGAGGCCCTAGAAGGAGAAGAGAGAGAGAAAGGGGCAGAAAACTTATTTGAAAA
AATAATGGCAGAAAATTTCTTTATTCTGGGGAAGGAAACAGACAACCACATCCAGGAAGCTCAGAAAGTTCCAAATAAGA
TGAATGTAAAGAGACCCACACTAAGACACATAATTAAATTGTCAAAAGTTAAAGACAAGGAACCTTAAAAGCAGCTAGAG
AAAAACAACTTGTTATGTACAAAGGAGCCCCCATAAAAAATCAGCAGATTTTTCAGCAGCAATTTTGCAAGCCAGAAGGA
AATGGCATGATACATTCAAAGGGCTGAAAGAAAAAACTGCCAACCAAGAATGCTCTACCTGGCAATGCTGTCCTTCAGAA
CTGAAGAGGAGATAACGAGTTTTCCAGACAAGCAAAAGCTGAAGGAGTTC

Alignment

ORF - retro_ecab_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.91 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SENFSKETENIRKYQIEVTELKNTPTELKNTIEGFKSRLDDTEERISGLEDRAVELIQSELSTQNRLEDL
          ..N..KE.ENI.K.Q.E.TEL.NT.TELKNT.EGFKSRLD..EERI..L.DRAVE.IQSE..........
Retrocopy NKNLNKERENITKHQTEITELRNTVTELKNTVEGFKSRLDEAEERITKLKDRAVEFIQSEQXXXXXXXXX

Parental  APSPKDCADSMRKCSIRTIGVQEGEEKEDGAESVLKEIIAENFPNLGDEREMCVEEVFRSPRYVNVKRPT
          ..S..D.........I..I...EGEE.E.GAE.....I.AENF..LG.E......E....P...NVKRPT
Retrocopy XXSLRDLRHNIKWTNIHHIEALEGEEREKGAENLFEKIMAENFFILGKETDNHIQEAQKVPNKMNVKRPT

Parental  ARHIVVKLAKMNDKE-RILRAARLKKITYKGTPI-RLSVDFSAETLQARTDWNDIFKTLKD-KNLQPRIL
          .RHI..KL.K..DKE.....A.......YKG.PI...S.DFSA..LQAR..W.D.FK.LK..KN.QPR.L
Retrocopy LRHI-IKLSKVKDKE<TLKAAREKQLVMYKGAPI<KKSADFSAAILQARRKWHDTFKGLKE<KNCQPRML

Parental  YPAKISFRYEGEIKSFPEKQKLRDF
          Y.A..SFR.E.EI.SFP.KQKL..F
Retrocopy YLAMLSFRTEEEITSFPDKQKLKEF

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	0.05 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.05 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.03 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_934 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_934 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005242	2 retrocopies	retro_ecab_192, retro_ecab_934 ,
Equus caballus	ENSECAG00000006639	4 retrocopies	retro_ecab_274, retro_ecab_484, retro_ecab_671, retro_ecab_689,