RetrogeneDB ID: retro_ecab_464

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:52761223..52761655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000006469
• Aliases: None
• Description: None

Sequence

>retro_ecab_464
ATGCCCAAGAATAAAGGTAAAAGAGGTAAATTAGATGCAGAGGTAAGAATGAGAATTCATCTAAAGAAAAGAGAGCTGGC
GCTCAAAGAGGATGGACAAGAGTATGCTCAAGTAATGAAAATGTTGGGAAATGGATGATTAGAAGTGAGGTGTTTTGATG
GCATAAATAGGTTAGGTCACATGAGAGGGAAATTGAGGAAAAAGCTTTGGATAAATACCTCAGATCTTATATTGGTTGCT
CTATGAGACTAACAGGATAACAAAGCTGGTGTAATTTTAAAACCCAATCAGGATGAAGCTATAAGTGTGAAGGCCTATGG
TGAGCTTCCAGAACATGCTAAATTTAAGGAAACTGATACATTTGGTCCTGGAGATGATGATGGAATTCAGTTTGATGATA
TTGGAAATGATGAAGAAGACATTGATGATATC

Alignment

ORF - retro_ecab_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKN-RRRGKNENESE-KRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGIKRLCHIRGKLRKK
          MPKNKGK.GK..R.RGKNEN.S..KREL..KEDGQEYAQV.KMLGNG.LE..CFDGI.RL.H.RGKLRKK
Retrocopy MPKNKGKRGKL<RCRGKNENSSK>KRELALKEDGQEYAQVMKMLGNG*LEVRCFDGINRLGHMRGKLRKK

Parental  VWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDD
          .WINTSD.ILV.L.D.QDNKA.VILK.N.DEA.S.KAYGELPEHAK..ETDTFGPGDDD.IQFDDIG.D.
Retrocopy LWINTSDLILVAL*D*QDNKAGVILKPNQDEAISVKAYGELPEHAKFKETDTFGPGDDDGIQFDDIGNDE

Parental  EDIDDI
          EDIDDI
Retrocopy EDIDDI

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	15.41 RPM
SRP021940_cerebellum	0.00 RPM	17.35 RPM
SRP021940_embryo	0.03 RPM	18.92 RPM
SRP021940_placental_villous	0.05 RPM	21.70 RPM
SRP021940_synovial_membrane	0.00 RPM	11.39 RPM
SRP021940_testis	0.06 RPM	11.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_464 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_464 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464 , retro_ecab_634,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,