RetrogeneDB ID: retro_ecab_283

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:40083976..40084644(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000016714
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TWSG1
• Ensembl ID: ENSECAG00000018189
• Aliases: None
• Description: twisted gastrulation homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:12429]

Sequence

>retro_ecab_283
GTGAAGTCACACCGTGTTGTTATGCTTACTCTAGCTGTCCTGGGGTTGCTGACATGGGTCCCCGTGTCACTGAGTTGCAA
TAAAGCTCTCTGTGCTGGTGATGTGAGCAAATGCCTAATTCAGGAGCTTTGCCAGTGCCGACCCGGAGAAGGGAATTGTT
CCTGCTGTAAGGAGTGCATGCTGTGTCTTGGAACCCTTTGGGATGAGTGCTGTGATTGCGTTGGTACGTGTAATCCTCGA
AATTATAGTGACATACCTCCAACTTCAAAGAGCACGGTGGAAGAGCTTCATGAGCCCATCCCTTCTCTCTCCCGGGCTCT
CACAGAAGGAGATACTCAGTTGAACTGGAACATCGTTTCCTTCCCTGTTGCAGAAGAACTTTCACATCATGAGAATCTGG
TTTCATTTTTAGAAACAGTGAACCAGCCACACCACCAAACTGTGTCTGTTCCCAGCAATATGTTCACGCACCTTATTCCA
GTGACAAAGAACACATGTGTATTGTGGTTTACTTTGATGACTGCGTGTCCATACATCGGTGTAAAATATTCTGTGAGTCC
ATGGGGGCAGCCAAATACCGCTGGTTCCATAACGCCTGCTGCGAGCGCATTGGTCCAGAGTGTATCGACTATGGTAGTAA
GACTGTCAAATGTATGAACTGCACGTTC

Alignment

ORF - retro_ecab_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSHCVVMLTLAVLVLLTWVPVSLSCNKALCASDVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC
          .KSH.VVMLTLAVL.LLTWVPVSLSCNKALCA.DVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC
Retrocopy VKSHRVVMLTLAVLGLLTWVPVSLSCNKALCAGDVSKCLIQELCQCRPGEGNCSCCKECMLCLGTLWDEC

Parental  CDCVGMCNPRNYSDTPPTSKSTVEELHEPIPSLFRALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV
          CDCVG.CNPRNYSD.PPTSKSTVEELHEPIPSL.RALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV
Retrocopy CDCVGTCNPRNYSDIPPTSKSTVEELHEPIPSLSRALTEGDTQLNWNIVSFPVAEELSHHENLVSFLETV

Parental  NQPHHQNVSVPSN-NVHAPYSSDKEHMCTVVYFDDCMSIHQCKISCESMGASKYRWFHNACCECIGPECI
          NQPHHQ.VSVPSN..VHAPYSSDKEHMC.VVYFDDC.SIH.CKI.CESMGA.KYRWFHNACCE.IGPECI
Retrocopy NQPHHQTVSVPSN<YVHAPYSSDKEHMCIVVYFDDCVSIHRCKIFCESMGAAKYRWFHNACCERIGPECI

Parental  DYGSKTVKCMNCMF
          DYGSKTVKCMNC.F
Retrocopy DYGSKTVKCMNCTF

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	48.88 RPM
SRP021940_cerebellum	0.00 RPM	7.43 RPM
SRP021940_embryo	0.00 RPM	31.51 RPM
SRP021940_placental_villous	0.19 RPM	17.27 RPM
SRP021940_synovial_membrane	0.00 RPM	30.06 RPM
SRP021940_testis	0.00 RPM	7.23 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_283 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_283 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002791	1 retrocopy	retro_dnov_783,
Equus caballus	ENSECAG00000018189	1 retrocopy	retro_ecab_283 ,