RetrogeneDB ID: retro_ecab_278

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:16389478..16389901(+)
• Located in intron of: ENSECAG00000022951

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000022034
• Aliases: None
• Description: None

Sequence

>retro_ecab_278
AAGAGAGAAAGAAGGATGGAGAGAATATTTGAAGAAATAACAGCTGAAATCTTCCAAAATTTGATGAACTATATGAATAC
AAACATCCAAGAAGCTCAAGAAATTCCAAGTAAGATGAACTCAAAGAGACCCACACCAAGACATTATAATCAACTTCTGA
AAGACAAAGACAGAGTATCTTGAAAGCAGCAAGAGAGAAGCAAATCATCACATACAAGGGATCCTCAATAAGATTATCAG
CATATTTCTCATCAGAAACTTTGGAGGCCAGAAGGCAGTGGGCTCATATATTCAAAGTGCTCAAAGAAGAAAACTGTAAA
CCAAGAATCCTATATTTTGGCAAAACTCTCCTTCAAAAGTGAGGGAGAAATTAAGACATTTCCATATACACAAAAGTTGA
GGGAGTTTGTTACCACTAGACCT

Alignment

ORF - retro_ecab_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.22 %
• Parental protein coverage: 59.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERDKGTEKLFEEIIAN-FPNLRKGTDIQTQEAQRAPNKINPKRPTPRHIIIKMSVIKDKERFLKATRER-
          .R....E..FEEI.A..F.NL........QEAQ..P.K.N.KRPTPRH........KDK.R......ER.
Retrocopy KRERRMERIFEEITAEIFQNLMNYMNTNIQEAQEIPSKMNSKRPTPRHY---NQLLKDKDRVS*KQQER<

Parental  KQNLTSRGSSIRFSADFPSETLEARRQWAGIFKVLKEKNCQPRILR-PAKLPFKSEGDIRTFP--NKLGE
          KQ..T..GSSIR.SA.F.SETLEARRQWA.IFKVLKE.NC.PRIL...AKL.FKSEG.I.TFP...KL.E
Retrocopy KQIITYKGSSIRLSAYFSSETLEARRQWAHIFKVLKEENCKPRILY>LAKLSFKSEGEIKTFPYTQKLRE

Parental  FITTRP
          F.TTRP
Retrocopy FVTTRP

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	0.03 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_278 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_278 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010030	21 retrocopies	retro_ecab_1021, retro_ecab_1023, retro_ecab_1035, retro_ecab_1071, retro_ecab_1089, retro_ecab_136, retro_ecab_182, retro_ecab_201, retro_ecab_281, retro_ecab_306, retro_ecab_486, retro_ecab_521, retro_ecab_537, retro_ecab_582, retro_ecab_590, retro_ecab_658, retro_ecab_670, retro_ecab_722, retro_ecab_786, retro_ecab_974, retro_ecab_996,
Equus caballus	ENSECAG00000016527	5 retrocopies	retro_ecab_214, retro_ecab_642, retro_ecab_879, retro_ecab_888, retro_ecab_993,
Equus caballus	ENSECAG00000020332	9 retrocopies	retro_ecab_1018, retro_ecab_117, retro_ecab_125, retro_ecab_346, retro_ecab_54, retro_ecab_604, retro_ecab_774, retro_ecab_775, retro_ecab_878,
Equus caballus	ENSECAG00000022034	4 retrocopies	retro_ecab_1039, retro_ecab_278 , retro_ecab_821, retro_ecab_858,
Equus caballus	ENSECAG00000023806	15 retrocopies	retro_ecab_1040, retro_ecab_1050, retro_ecab_1073, retro_ecab_1077, retro_ecab_1108, retro_ecab_176, retro_ecab_241, retro_ecab_298, retro_ecab_339, retro_ecab_714, retro_ecab_778, retro_ecab_781, retro_ecab_852, retro_ecab_855, retro_ecab_953,