RetrogeneDB ID: retro_ecab_600

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:2242637..2243624(+)
• Located in intron of: ENSECAG00000006736

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS4
• Ensembl ID: ENSECAG00000015209
• Aliases: None
• Description: COP9 signalosome subunit 4 [Source:HGNC Symbol;Acc:16702]

Sequence

>retro_ecab_600
CCTGAGAGCACAGCCAAAGAAATCTATCATTTCACCTTGGAGAAGATCCAGCCTAGAGTCATTTCATTTGAGGAGCAGGT
TGTTTCCATAAGACAGCATCTTGCATCCATATATGAGAAAGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGAATTC
CTTTGGAAACAGGACAAAAAGAATACAATGTAGATTATAAACTGGAGACATACCTGAAGATTGCTAGGCTATATCTGGAG
GATGATGATCCCGTCCAGGCAGAGGCTTACATAAATTGAGCATCATTGCTTCAGAATGAATCAACCAACGAACAGTTACA
GATATATTATAAGGTATGCTATGCACGTGTTCTTGATTACAGAAGAAAATTCATTGAAGCTGCACAAAGGTACAGTGAGC
TCTCTTACAAGACAATAGTGCAGGAAAGTGAAAGACTAGAGGCCTTAAAACATGCTTTGCACTGTACCATCTTAGCATCA
GCAGGACAGCAGCGTTCTTGGATGCTAGCTACTCTTTTTAAGGAGGAAAGGTGCCAGCAACTTGCTGCTTATGGGATCCT
AGAGAAAATGTACCTAGATAGGATCATCAGAGGAAATCAACTTCAAGAATTTGCTGCCATGCTGATGCCTCACCAAAAAG
CAACCACAGCTGATGGTTCCAGCATTTTGGACAGAGCTGTTACTGAACACAATTTGTTGTCTGCAAGCAAATTATATAAT
AATATTACCTTCGAAGAACTTGGAGCTCTTTTAGAGATCTCTGCAGCTAAGGCAGAAAAGATAGCATCACAAATGATAAC
AGAAGGCCGTATGAATGGATTTATCGATCAGATTGATGGAATAGTTCATTTTGAAACACGAGAAGCCCTGCCAACATGGG
ACAAACAGATCCAATCACTTTGTTTCCAAGTGAATAACCTTTTGGAGAAAATTAGTCAGACAGCACCAGAATGGACAGCA
CAAGCCATGGAAGCCCAGATGGCTCAG

Alignment

ORF - retro_ecab_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.36 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLE
          P.STAKEIYHFTLEKIQPRVISFEEQV.SIRQHLASIYEKE.DWRNAAQVLVGIPLETGQK.YNVDYKLE
Retrocopy PESTAKEIYHFTLEKIQPRVISFEEQVVSIRQHLASIYEKE-DWRNAAQVLVGIPLETGQKEYNVDYKLE

Parental  TYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTI
          TYLKIARLYLEDDDPVQAEAYIN.ASLLQNESTNEQLQI.YKVCYARVLDYRRKFIEAAQRY.ELSYKTI
Retrocopy TYLKIARLYLEDDDPVQAEAYIN*ASLLQNESTNEQLQIYYKVCYARVLDYRRKFIEAAQRYSELSYKTI

Parental  VHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLM
          V.ESERLEALKHALHCTILASAGQQRS.MLATLFK.ERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLM
Retrocopy VQESERLEALKHALHCTILASAGQQRSWMLATLFKEERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLM

Parental  PHQKATTADGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQID
          PHQKATTADGSSILDRAV.EHNLLSASKLYNNITFEELGALLEI.AAKAEKIASQMITEGRMNGFIDQID
Retrocopy PHQKATTADGSSILDRAVTEHNLLSASKLYNNITFEELGALLEISAAKAEKIASQMITEGRMNGFIDQID

Parental  GIVHFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
          GIVHFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Retrocopy GIVHFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ

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	0.65 RPM
SRP021940_cerebellum	0.00 RPM	1.40 RPM
SRP021940_embryo	0.13 RPM	0.97 RPM
SRP021940_placental_villous	0.00 RPM	1.15 RPM
SRP021940_synovial_membrane	0.11 RPM	0.47 RPM
SRP021940_testis	0.00 RPM	1.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_600 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_600 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	ENSECAG00000015209	2 retrocopies	retro_ecab_315, retro_ecab_600 ,
Monodelphis domestica	ENSMODG00000019311	1 retrocopy	retro_mdom_824,
Mustela putorius furo	ENSMPUG00000014708	1 retrocopy	retro_mputfur_1010,
Otolemur garnettii	ENSOGAG00000027198	1 retrocopy	retro_ogar_3514,
Tupaia belangeri	ENSTBEG00000017599	2 retrocopies	retro_tbel_2134, retro_tbel_53,