RetrogeneDB ID: retro_ecab_915

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:77912658..77913198(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000000947
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCTD
• Ensembl ID: ENSECAG00000017516
• Aliases: None
• Description: dCMP deaminase [Source:HGNC Symbol;Acc:2710]

Sequence

>retro_ecab_915
CCCAACATGAGTGAAGTGTCCTGGAGAAAACGTGATGACTATTTGCAGTGGCCTGAGTATTTCATGGCGGTGGCCTTCCT
ATCGGCACAGAGAAGCAAAGATCCAAATTCGCAGGTTGCAGCCTGCATCGTGAATGCAGAAAACAAGATTGTCGGGATTG
GGTACAATGGAATGCCAAATGGGTGCAGCGATGACCTGTTGCCTTGGAGGAGGACAGCGGAGAATAAGCTGGATACCAAA
TACCCTTACGTGTGCCATGCCGAGCTCAATGCCATTATGAACAAAAACTCGGCCGACGTGAAGGGCTGTACCATGTACGT
CGCCTTGTTCCCGTGCAATGAGTGTGCTAAGCTCATCATCCAGACAGGTATCAAAGAAGTTATTTTCATGTCTGATAAAT
ACCATGATAGCGATGAGGCAACCGCTGCCAGGCTCTTGTTTGATATGGCTGGGGTTACCTTCAGGAAATTCACACCAAAG
TGCAGCAAGATTGTCATTGACTTTGATTCAATTAACAGCAGACCGACTCAGAAGCCTCAG

Alignment

ORF - retro_ecab_915 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PNMSEVSWRKRDDYLQWPEYFMAVAFLSAQRSKDPNSQVGACIVNAENKIVGIGYNGMPNGCSDDLLPWR
          PNMSEVSWRKRDDYLQWPEYFMAVAFLSAQRSKDPNSQV.ACIVNAENKIVGIGYNGMPNGCSDDLLPWR
Retrocopy PNMSEVSWRKRDDYLQWPEYFMAVAFLSAQRSKDPNSQVAACIVNAENKIVGIGYNGMPNGCSDDLLPWR

Parental  RTAENKLDTKYPYVCHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQAGIKEVIFMSDKYHDSDEA
          RTAENKLDTKYPYVCHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQ.GIKEVIFMSDKYHDSDEA
Retrocopy RTAENKLDTKYPYVCHAELNAIMNKNSADVKGCTMYVALFPCNECAKLIIQTGIKEVIFMSDKYHDSDEA

Parental  TAARLLFDMAGVTFRKFTPKCSKIVIDFDSINSRPTQKPQ
          TAARLLFDMAGVTFRKFTPKCSKIVIDFDSINSRPTQKPQ
Retrocopy TAARLLFDMAGVTFRKFTPKCSKIVIDFDSINSRPTQKPQ

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	5.67 RPM
SRP021940_cerebellum	0.00 RPM	0.88 RPM
SRP021940_embryo	1.56 RPM	7.39 RPM
SRP021940_placental_villous	0.63 RPM	5.10 RPM
SRP021940_synovial_membrane	2.69 RPM	8.07 RPM
SRP021940_testis	0.51 RPM	2.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_915 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017516	3 retrocopies	retro_ecab_829, retro_ecab_830, retro_ecab_915 ,
Mus musculus	ENSMUSG00000031562	1 retrocopy	retro_mmus_3672,
Rattus norvegicus	ENSRNOG00000013215	1 retrocopy	retro_rnor_2937,
Sarcophilus harrisii	ENSSHAG00000015218	1 retrocopy	retro_shar_124,
Tursiops truncatus	ENSTTRG00000001460	1 retrocopy	retro_ttru_613,