RetrogeneDB ID: retro_ecab_978

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:69781609..69782244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP3B
• Ensembl ID: ENSECAG00000008088
• Aliases: None
• Description: nipsnap homolog 3B (C. elegans) [Source:HGNC Symbol;Acc:23641]

Sequence

>retro_ecab_978
GGCCCCAGACAATATGATGGAACATTCTATGAATTTCATACTATTGCCTTAAACCCTCAAAGATAGATGAGTTTCTGGAA
AATATTAAGAAAAACCTTCATCTTTGAACAGCTCCCTCTGAATTGGTTGGATTATGGAGTGCAAAATTTGTAGGCAGAAT
GAATAAAGTGTTCCATGTTTGGAAGTATGATAGTTTTGCTCATCAAGGTGAAGTTTGGAAAGGCTTGGCCAAAAATAAGG
CATGCCAAGAACAACTTCTCATTCCAAATTTGGCTCTCATTGATAAACAAGAGTTTGAGATTACCTATGTGGTACCATGG
TGCAAAATAGAAAAACGTCCAAAAGGAGTCTATGAGCTTTCATCTGGTTATTTTCCAGATGAAACCTGGTGGGCCAGCTC
TGTGGGGTGATGCATTTAAAAGGACAGTTGATGCCCATGTCAATATAGGCTGCACAAAACTGTTGGCGTTGTCCACCCAG
AATATGGAGCACCCAGCAGAGATCATGTTCTTTGGTGAATGAGAGTGCAGATAGTCATGCAGCTGGAGACATCAATTTCA
TGAAGATCTTAACTTGCGGTGGCTGTTTGGGAAAACCTCAACTACCAAATGTCACATAAAAATATGCTTCTGATT

Alignment

ORF - retro_ecab_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.12 %
• Parental protein coverage: 92.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GPRQYDGTFYEFRT-YCLKPSKMNEYMEKIKKNIHLRTAHSELVGFWSVEFGGRMNKVFHIWKYDNFAHR
          GPRQYDGTFYEF.T.YCLKPSK..E..E.IKKN.HL.TA.SELVG.WS..F.GRMNKVFH.WKYD.FAH.
Retrocopy GPRQYDGTFYEFHT<YCLKPSKIDEFLENIKKNLHL*TAPSELVGLWSAKFVGRMNKVFHVWKYDSFAHQ

Parental  TEVRKALAKDREWQEQFLIPSLALIDKQEFEIAYLVPWSKLEKPP-KEGV-YELATFQMKPGGPALWGEP
          .EV.K.LAK....QEQ.LIP.LALIDKQEFEI.Y.VPW.K.EK.P.KE.....L..FQMKPGGPALWG..
Retrocopy GEVWKGLAKNKACQEQLLIPNLALIDKQEFEITYVVPWCKIEKRP>KESMSFHLVIFQMKPGGPALWGDA

Parental  FKRAVNAHVNRGYSKL-VGVFHTEYGTLNRVHVLW-WNESADSRAAG-RHESHEDPR-VVAAVRESVNYL
          FKR.V.AHVN.G..KL.VGV.H.EYG...R.HVLW..NESADS.AAG.RH..HED......AV.E..NY.
Retrocopy FKRTVDAHVNIGCTKL<VGVVHPEYGAPSRDHVLW<VNESADSHAAG<RHQFHEDLN<LAVAVWENLNYQ

Parental  VSQQNMLLI
          .S..NMLLI
Retrocopy MSHKNMLLI

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	2.66 RPM
SRP021940_cerebellum	0.00 RPM	3.95 RPM
SRP021940_embryo	0.00 RPM	4.01 RPM
SRP021940_placental_villous	0.00 RPM	3.70 RPM
SRP021940_synovial_membrane	0.00 RPM	2.96 RPM
SRP021940_testis	0.00 RPM	1.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_978 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_978 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_295

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Ailuropoda melanoleuca	ENSAMEG00000005118	1 retrocopy	retro_amel_552,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Equus caballus	ENSECAG00000008088	1 retrocopy	retro_ecab_978 ,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Mustela putorius furo	ENSMPUG00000007103	1 retrocopy	retro_mputfur_1471,