RetrogeneDB ID: retro_ecab_780

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:28300981..28301410(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGTA
• Ensembl ID: ENSECAG00000010381
• Aliases: None
• Description: small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha [Source:HGNC Symbol;Acc:10819]

Sequence

>retro_ecab_780
GGCCTGCGCGGTCTATGTCTGTACCAGAGCTTCCGCACAAGCACACTGAACTACTACTACGAGGAGGCCTTGGAGCTGGG
CCCGGACTAGAAGACTTGCAAGTCGAATCTCAAGATAGCCAACTGAAGCTGAGAGAGGGCCAAGTCCCACAGGAAGCTTT
GACATCACCGGCAAGCTGAAGAACCCAAGCTTCAGGAGCATGGCGTCAAACCTAATGAACAATCCCCAAGTTCAACAGCT
CATGTCTGGGATGATTTCGGTGGCCATAAACACTTAGGGACTCCTGGCACCAACCCTTCACAGAAAGACCTGGCCAATCT
CATCCAGGCGGGCCAGGAGTTCGTTCAGCAGATGCAGCAGCAAAATCCAGAGTTGACAGAACAGCTCAGAAGTCAGACCC
CCAGGGCCAACAAGGATGACCTGCAGGAA

Alignment

ORF - retro_ecab_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.53 %
• Parental protein coverage: 69.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRMGLALSSLNKHTEAVAYYKKALELDPDNEKYKSNLKIA-ELKLQEGT-SPTGGVGSFDIAGLLNNPSF
          G..GL.L...........YY..ALEL.PD....KSNLKIA..LKL.EG..SPT...GSFDI.G.L.NPSF
Retrocopy GLRGLCLYQSFRTSTLNYYYEEALELGPD*KTCKSNLKIA<QLKLREGQ<SPT---GSFDITGKLKNPSF

Parental  MSMASNLMNNPQVQQLMSGMIS-GGHNPLGTPGTSPSQNDLASLIQAGQQFAQQMQQQNPELIEQLRSQI
          .SMASNLMNNPQVQQLMSGMIS.GGH..LGTPGT.PSQ.DLA.LIQAGQ.F.QQMQQQNPEL.EQLRSQ.
Retrocopy RSMASNLMNNPQVQQLMSGMIS<GGHKHLGTPGTNPSQKDLANLIQAGQEFVQQMQQQNPELTEQLRSQ-

Parental  RSRTPSASNDDQQE
          ...TP.A..DD.QE
Retrocopy ---TPRANKDDLQE

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	14.17 RPM
SRP021940_cerebellum	0.05 RPM	31.63 RPM
SRP021940_embryo	0.00 RPM	40.89 RPM
SRP021940_placental_villous	0.05 RPM	15.06 RPM
SRP021940_synovial_membrane	0.00 RPM	16.39 RPM
SRP021940_testis	0.00 RPM	53.65 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_780 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005257	1 retrocopy	retro_amel_1169,
Equus caballus	ENSECAG00000010381	2 retrocopies	retro_ecab_723, retro_ecab_780 ,
Monodelphis domestica	ENSMODG00000004900	1 retrocopy	retro_mdom_277,
Mus musculus	ENSMUSG00000004937	1 retrocopy	retro_mmus_621,
Sarcophilus harrisii	ENSSHAG00000011900	1 retrocopy	retro_shar_39,