RetrogeneDB ID: retro_ecab_50

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:45976319..45977120(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001560
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSECAG00000025151
• Aliases: None
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_ecab_50
ATGCTGCTGCTGGCCCTGGCACCCAGGGCTTGGCTCAGGCTCCCTCAGCTGAAGCGCCTGGTCTGCCCTAGGACCCTGGG
AGGTGATTCCCTACGCATGAGGTGCCAGCTCTTGTCAAGGCAGGGTCCTGCAGAGACAGGCAAACAGGGCCAGCCCCAGG
GCCCTGGGCTTCGAACTAGGTTGCTGATCACAGCCTTGTTTGGGGCTGGGCTGGGTGGGGCCTGGCTGGCTGCAAGGGCT
AAGAAGGAGCAGTGGCGGCAGCAACGGCGGACAGAAGCCCTGCGTCAGGCAGCCGTGGGCCAGGGCGACTTCAGTCTGCT
GGACCACCGGGGCCAGGCTCGCTGCAAAGCTGACTTCCGGGGCCAGTGGGTACTGATGTACTTTGGCTTTACTCACTGCC
CTGACATCTGCCCAGATGAGCTGGAGAAGTTGGTGCAGGTGGTACAGCAGCTGGAAGCTGAGCCTGGCCTGCCCCTGGTG
CAGCCCATCTTCATTACTGTGGACCCTGAGCGGGACAGCGTCGAGGCCATGGCCCGCTATGTGCAGGACTTCCACCCGAG
GCTGCTGGGCCTGACTGGCTCTGCCGAGCAGATTGCTCAGGCTAGCCACAACTACCGTGTATACTACAGTGCTGGCCCCA
AAGACGAGGACCAGGATTACATTGTGGATCACTCCATTGCTATCTACCTGCTTAACCCTGATGGCCTCTTCACAGACTAC
TATGGCCGGGCCAGGTCAGCTGAGCAGATTGCAGACAGCGTGCGGCACCACATGGCTACCTTCCGCAGTGTCCTGCCCTG
A

Alignment

ORF - retro_ecab_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.51 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIGGALLAGMKYFKKEKTEKLEKQRQ-RSIGKPLLG-GPFSLTTHTGESKTDKDYLGQWVLIYFGFTHCP
          A..GA.L.G.......K.E....QR..........G.G.FSL..H.G......D..GQWVL.YFGFTHCP
Retrocopy ALFGAGLGGAWLAARAKKEQWRQQRRTEALRQAAVGQGDFSLLDHRGQARCKADFRGQWVLMYFGFTHCP

Parental  DVCPEELEKMIQVVDEIDSIPTLPDLTPLFITIDPERDTKEAIANYVKEFSPKLIGLTGTKEEIDQVARA
          D.CP.ELEK..QVV......P.LP...P.FIT.DPERD..EA.A.YV..F.P.L.GLTG..E.I.Q....
Retrocopy DICPDELEKLVQVVQQLEAEPGLPLVQPIFITVDPERDSVEAMARYVQDFHPRLLGLTGSAEQIAQASHN

Parental  YRVYYSPGPKDEDEDYIVDHTIIMYLIGPNGEFLDYFGQNKKNAEIAGSIAAHMREHR
          YRVYYS.GPKDED.DYIVDH.I..YL..P.G.F.DY.G.......IA.S...HM...R
Retrocopy YRVYYSAGPKDEDQDYIVDHSIAIYLLNPDGLFTDYYGRARSAEQIADSVRHHMATFR

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	4.25 RPM	5.78 RPM
SRP021940_cerebellum	14.80 RPM	6.28 RPM
SRP021940_embryo	11.41 RPM	6.50 RPM
SRP021940_placental_villous	7.26 RPM	7.31 RPM
SRP021940_synovial_membrane	8.87 RPM	5.49 RPM
SRP021940_testis	27.62 RPM	3.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_50 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_50 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50 ,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,