RetrogeneDB ID: retro_ecab_554

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:32126104..32126710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN17
• Ensembl ID: ENSECAG00000022322
• Aliases: None
• Description: tetraspanin 17 [Source:HGNC Symbol;Acc:13594]

Sequence

>retro_ecab_554
TTTGTAGTAGTAGGAGGCATCATGTCTGTGCTGGGCTTTGCCGGCTGCAGAGGGGCTCTCCAGGAGAACACCTGCCTGCT
CAAGTTTTTCTCCGTGTTTCTTGGCCTCATCTTCTTCCTGGAGCTGGCGACAGGGATCCTGGCCTTTGTCTTCAAGGACT
GGATTCGAGACCAGCTCCACCTCTTCATCAACAACAACGTCAAGGCCTATCGGGACGACATTGACCTCCAGAACCTCATT
GACTTTGCTCAAGAATACTGGTCTTGCTGCAGAGCCCGAGGGCCCAACGACTGGAACCTCAATATCTACTTCAACTGCAC
TGACTTGAACCCGAGCCGGGAGCGCTGCAGGGTGCCCTTCTCTTGCTGCGTCAGGGACCCTGCGGAAGATGTCCTCAACA
CCCAGTGTGGCTACGATGTCTGGCTCAAACTGGAGCTGGAGCAGCAGGGCTCTATCCACACCAAAGGCTGCGTGGGCCAG
TTCGAGAAGTGGCTGCAGGACAACCTGATCGTCGTGGCTGGGGTCTTTGTGGGCATCGCCCTCTTCCAGATCTTCGGTAT
CTGCCTGGCCCAGAACCTCGTGAGCGACATCAAGGCAGTGAAGGCC

Alignment

ORF - retro_ecab_554 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 79.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVVVGGIMSVLGFAGCIGALRENTFLLKFFSVFLGLIFFLELATGILAFVFKDWIRDQLNLFINNNVKAY
          FVVVGGIMSVLGFAGC.GAL.ENT.LLKFFSVFLGLIFFLELATGILAFVFKDWIRDQL.LFINNNVKAY
Retrocopy FVVVGGIMSVLGFAGCRGALQENTCLLKFFSVFLGLIFFLELATGILAFVFKDWIRDQLHLFINNNVKAY

Parental  RDDIDLQNLIDFAQEYWSCCGARGPNDWNLNIYFNCTDLNPSRERCGVPFSCCVRDPAEDVLNTQCGYDV
          RDDIDLQNLIDFAQEYWSCC.ARGPNDWNLNIYFNCTDLNPSRERC.VPFSCCVRDPAEDVLNTQCGYDV
Retrocopy RDDIDLQNLIDFAQEYWSCCRARGPNDWNLNIYFNCTDLNPSRERCRVPFSCCVRDPAEDVLNTQCGYDV

Parental  RLKLELEQQGSIHTKGCVGQFEKWLQDNLIVVAGVFVGIALLQIFGICLAQNLVSDIKAVKA
          .LKLELEQQGSIHTKGCVGQFEKWLQDNLIVVAGVFVGIAL.QIFGICLAQNLVSDIKAVKA
Retrocopy WLKLELEQQGSIHTKGCVGQFEKWLQDNLIVVAGVFVGIALFQIFGICLAQNLVSDIKAVKA

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	3.84 RPM
SRP021940_cerebellum	0.00 RPM	13.35 RPM
SRP021940_embryo	0.31 RPM	24.19 RPM
SRP021940_placental_villous	0.10 RPM	19.82 RPM
SRP021940_synovial_membrane	0.05 RPM	19.63 RPM
SRP021940_testis	0.19 RPM	23.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_554 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007218	2 retrocopies	retro_amel_1365, retro_amel_979,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585, retro_cfam_704,
Callithrix jacchus	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289,
Equus caballus	ENSECAG00000022322	1 retrocopy	retro_ecab_554 ,
Felis catus	ENSFCAG00000007803	1 retrocopy	retro_fcat_1133,
Mustela putorius furo	ENSMPUG00000012505	1 retrocopy	retro_mputfur_428,