RetrogeneDB ID: retro_ecab_615

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:18005246..18005913(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ecab_615
GAAATGAAGAATACAATACTGGAAATGAAAAATTCACTAGAGGGACTCAATAGCAGAGTAGATGATACAGAAGAATGGAT
TAGTGAGCTGGATGAAAGAGTAGAGGAAATCACCCAAGCTGAACAGATAAAAGAAAAAAGAATTAGACATAATGAGAACA
ATCTAAGGGAACTCTGAGACAATATCAAGTGCACTAACATTCATATAATAGGTGTCCCAGGAGAAGAGAGGGGAAGAGAA
TCTATTTGAAGAAATAATAGCTGAAAACTTTCCTAATCTAAGGAAGGAAACAGACATTCAAGTACAGGAAGCACAGAGAG
CACCAAACAAGATGAACACCAAGAGGCCCACACGAAGACACATTATAATTAAAATACCCAAAATTAAAGATAAAGAGAGA
ATCCTAAAAGCAGCAAGAGAAAGGCAACAAGTGACAGACAAAGGAAAGCCCATAAGGCTATCAGTGGACTTCTCAGCCGA
AACCCTACAGGCTAGAAGAGAGTGGCATGACATATTTAACGTGCTGAAGGGAAAAAACCAACAGCCGAGAATACTCTATC
CAACATGGTTATTCAGAATGGAAGGAGACATAAAGAACTTCCTAGACAAGCAAAAATTAAAGGAGTTTATCACCAAGAAA
CCAGTTCTACAAGAAATGCTGAAAGGG

Alignment

ORF - retro_ecab_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVKSAITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVI
          E.K..I.E.K.SL.G.NSR....EE.I..LD...EEIT.AEQ..EKRIR.NEN.LREL.DNIKC.NIH.I
Retrocopy EMKNTILEMKNSLEGLNSRVDDTEEWISELDERVEEITQAEQIKEKRIRHNENNLREL*DNIKCTNIHII

Parental  GVPEERQRGRK-LFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAA
          GVP.E..RGR..LFEEIIAE.FPNLRKETD.QVQEAQR.PNK...KRPT.RHIIIK..KIKDKERILKAA
Retrocopy GVPGE-ERGRE>LFEEIIAENFPNLRKETDIQVQEAQRAPNKMNTKRPTRRHIIIKIPKIKDKERILKAA

Parental  RERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQDKQKLK
          RERQQVT.KGKPIRLSVDFSA.TLQ.RREWHDIF.V.K.KN.QPRILYP..L.F.MEG.IK.F.DKQKLK
Retrocopy RERQQVTDKGKPIRLSVDFSAETLQARREWHDIFNVLKGKNQQPRILYPTWL-FRMEGDIKNFLDKQKLK

Parental  EFITKKPILQEMLKG
          EFITKKP.LQEMLKG
Retrocopy EFITKKPVLQEMLKG

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	0.05 RPM	0.00 RPM
SRP021940_synovial_membrane	0.08 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_615 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_615 has 0 orthologous retrocopies within eutheria group .

---

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,