RetrogeneDB ID: retro_ecab_583

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:43140287..43140970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF167
• Ensembl ID: ENSECAG00000021567
• Aliases: None
• Description: ring finger protein 167 [Source:HGNC Symbol;Acc:24544]

Sequence

>retro_ecab_583
CCTGCGGCCTTCCCACTTCCTGTGGTTGCACCCCTGGGCTGTGGGGAGCGGCCCCTACCTGAGGGCGCTTTGGAGCTGTT
TTGGACCACAGTGCCTGCGTGGACTTTGCCGACCTCCCAACTCTCTTTGAGGCTGCCTTGAGACAGGAGGGCCGTCAGGG
CTTCCTTGTGGAGGCTCACCCAGCGAATGCCAGCAGCCCCATTGCCCCACCACTCCCAGCCTCCGTCAACGGGTCAGTCT
TTGTTGGGCTGTTTCGAAGATTCGACTCCAACTTTGCCCTCAAGGTCCTATAGGCTCAGAAGCCTGAGTATGATGCAGCT
GTGGCACACAATGTGAATTCCCGTGAACTTCTGAACATGGGGTGGACTCAGGAGGAAATTCAGCAGCAGATTTGCATCTC
ATCTGTGTTTATCAGGGAAAGGAGCACCAAGCGCCTGCGTGCCATTTTGGTCTACCAGAAGGGGGCTCAGGTGCTTCTGG
TCCCAGACAATAGCTTCCTCTTGGGCTGTTGCCTCATCCTTTTTACAGGGATTGTGGGACTGCTAATTTTGGCCATGGGA
GCAATGGCGCTAGCTCACTGTATCTGGTCCCAGAAGCAGCTCCAGCAGAATCAATTGACCAAAGAGCAACTGAAACAGCT
TCCTACACATGACTATCAGAAGGGAGACCAGTATGACATCTGT

Alignment

ORF - retro_ecab_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.62 %
• Parental protein coverage: 65.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAAFQLPVVV-ATVLWGAAPIRGLIRATSDHNASMDFADLPALFGAALSQEGLQGFLVEAHPANACSPIA
          PAAF.LPVV.....LWGAAP..G...A..DH.A..DFADLP.LF.AAL.QEG.QGFLVEAHPANA.SPIA
Retrocopy PAAFPLPVVA<TPGLWGAAPT*GRFGAVLDHSACVDFADLPTLFEAALRQEGRQGFLVEAHPANASSPIA

Parental  PPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFIG
          PP.PA.VNGSVF..L.RRFD.NF.LKVL.AQK..Y.AAV.HNVNS.ELLNM.W..EEIQQQI.I.SVFI.
Retrocopy PPLPASVNGSVFVGLFRRFDSNFALKVL*AQKPEYDAAVAHNVNSRELLNMGWTQEEIQQQICISSVFIR

Parental  ERSSEYLRALFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGAVMIVRCIQHRKRLQRNRLTKE
          ERS...LRA..VY.KGA.VLLVPDNSF.LG..LI.FTGIVGLL.LAMGA.....CI...K.LQ.N.LTKE
Retrocopy ERSTKRLRAILVYQKGAQVLLVPDNSFLLGCCLILFTGIVGLLILAMGAMALAHCIWSQKQLQQNQLTKE

Parental  QLKQIPTHDYQKGDQYDVC
          QLKQ.PTHDYQKGDQYD.C
Retrocopy QLKQLPTHDYQKGDQYDIC

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	41.26 RPM
SRP021940_cerebellum	0.00 RPM	69.23 RPM
SRP021940_embryo	0.00 RPM	52.09 RPM
SRP021940_placental_villous	0.00 RPM	80.06 RPM
SRP021940_synovial_membrane	0.00 RPM	50.70 RPM
SRP021940_testis	1.98 RPM	106.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_583 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_583 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_84
Sus scrofa	retro_sscr_518

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583 ,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,