RetrogeneDB ID: retro_ecab_400

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:60137129..60137819(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003783
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UCHL3
• Ensembl ID: ENSECAG00000024190
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12515]

Sequence

>retro_ecab_400
ATGGAGGGTCAGCGCTGGCTCCCGTTGGAGGCCAATCCCGAGGTCACCAACCAGTTTCTCAAACAATTAGGTCTACATCC
TAACTGGCAGTTTGTTGATGTATATGGAATGGATCCTGAACTCCTTAGCATGGTTCCACGGCCAGTGTGCGCAGTGTTAC
TTCTCTTCCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAGGAAAAAATAAAATCTCAGGGACAAGATGTT
ACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATCCATGCTATTGCCAACAA
TAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAGTCTGTGTCCATGAGCCCTGAAGAAC
GAGCCAGATACCTGGAGAACTATGACGCTATTCGAGTTACTCACGAGACCAGTGCCCATGAAGGTCAGACTGAGGCCCCG
AGTCCAGATGAAAAGGTAGACCTTCATTTCATTGCGTTAGTTCACGTGGATGGGCATCTCTATGAATTAGATGGACGGAA
ACCATTTCCAATTAATCACGGGGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGG
AACGTGACCCTGATGAATTAAGATTCAATGCAATTGCTCTTTCTGCAGCA

Alignment

ORF - retro_ecab_400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEE
          MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEE
Retrocopy MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEE

Parental  EKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLEN
          EKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLEN
Retrocopy EKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLEN

Parental  YDAIRVTHETSAHEGQTEAPSPDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCK
          YDAIRVTHETSAHEGQTEAPSPDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCK
Retrocopy YDAIRVTHETSAHEGQTEAPSPDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCK

Parental  KFMERDPDELRFNAIALSAA
          KFMERDPDELRFNAIALSAA
Retrocopy KFMERDPDELRFNAIALSAA

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	0.24 RPM
SRP021940_cerebellum	0.10 RPM	0.62 RPM
SRP021940_embryo	0.20 RPM	0.82 RPM
SRP021940_placental_villous	1.49 RPM	4.14 RPM
SRP021940_synovial_membrane	0.33 RPM	0.80 RPM
SRP021940_testis	0.70 RPM	1.60 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_400 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_400 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400 ,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227,