RetrogeneDB ID: retro_ecab_545

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:2849058..2849516(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000018840
• Aliases: None
• Description: None

Sequence

>retro_ecab_545
GAAGAGAGGGAGAGGGGGAAGAGAGTTTACTTAAAGAATTAAGAGCTGAAAACTTTCCAAACTTGGGGAAGGACTTTGAC
ATGCAAGTTCACAAAGCTAATAGAACACCCTATTATTTCAGTGCACAAACACCTTTTCCAAGACACATTATAATGAAACT
GTCAAAAATCAATGATAAAGAAAAAAATCTTGAAGGCAACCAGGAGTATAAGACAGTAATCTACAAAGGAATCCCCATTA
GGTATCAGTGGATTTCTCAGCAGAAACCCTATAGGCCAGGAGAGCGGAATGACATATTCAAAGTGTTGAAAGATATAAAT
TGCCAGCCAAGAATACTTTATCTGGCAAAGTTATCCTTCAGGTATGGAAGGGAAATTAATACTTTCCCAGACACATAAAA
GCTGAGGGAGTTCACCACCACTAGACCTGCCTTGAAAGAAATGCTCAAAGGACTTCTA

Alignment

ORF - retro_ecab_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.95 %
• Parental protein coverage: 76.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EERQNRR-ESLFKEIITENFLNLGKGLEIQVKEANRTPNYINVERPSPRHILVKLAKLVMKEYIMAEAAR
          EER.....ESL.KE...ENF.NLGK....QV..ANRTP.Y.....P.PRHI..KL.K...KE........
Retrocopy EERERGK<ESLLKELRAENFPNLGKDFDMQVHKANRTPYYFSAQTPFPRHIIMKLSKINDKEKNLEGNQE

Parental  QKKITYKGSPIRLSADFSQTVQTRREWNDIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFI
          .K...YKG.PIR......Q......E.NDI.K.LK..N..PRILY..KLSFRYGREI..F.D..KLREF.
Retrocopy YKTVIYKGIPIRYQWISQQKPYRPGERNDIFKVLKDINCQPRILYLAKLSFRYGREINTFPDT*KLREFT

Parental  TTRPPLQEMMKTAL
          TTRP.L.EM.K..L
Retrocopy TTRPALKEMLKGLL

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	0.03 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_545 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018840	28 retrocopies	retro_ecab_1000, retro_ecab_1011, retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327, retro_ecab_424, retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545 , retro_ecab_564, retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908, retro_ecab_928, retro_ecab_929,