RetrogeneDB ID: retro_ecab_980

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:80798639..80799414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YARS2
• Ensembl ID: ENSECAG00000011140
• Aliases: None
• Description: tyrosyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:24249]

Sequence

>retro_ecab_980
CAGACACGGCTGAAGACTCCTAGAGACATGAGCGCCAAGTTCTAATACCAGGTGCCCCAGGCTTGTGACTTCCATCATCA
GTTCCAGAGTATGGATGGTGGGTCCAGCTGGTGGACCTGATCAGCTGGGCAACATCATGTCCAGATACAAGTCAATCCAC
AAGTTGACTAGAGAAGACCATTTGGCATCCCTGTTGCTCTAATTACAAGCACAGCTGGAGCAGAACTGGGAAAGTCAGTG
GCAGTGCTGTCTGGATAAACAGAGATGAGACATCTCCATTTGAATTGTACCATTTCTTTGTCAGGGAGAAAGATGATTTG
GAAGAAAGGTAGCCGAAGCTCCTCACTTTTCTGCCGCTTCCAGAGCTTGACCACGTAATGTGGCTGCATGTCAAAGAGCC
ACAAAAGCAGGGTCCTCGGAAACGACTGGCTGCAGAAGTAACAAAGCTTGTACATGGACAGGAAGGGCTGGCTTCTGCTA
AAATGTGTAAACAAGCACTTTGTCATCGTTGTACAGACACACTGGAGGTCATGTCTGATCAAGAGATGAAAGAGTGTTTA
AAGAAGCTTCATTTTCTGAATTAGTTCTTGACCCTGGAGCAAGCGGCTGAGATACATGCCACAAAGCAAATGCCATTCCA
GATGGTCCCCGAAGGTATCAGGTGATAACACAGGGCAGAGTCAGTATAAGTCACAGATGAGTAACAAATCCTGAGAGTGT
TTTAGTGGTTGGACAACATATTCTTAAGAATGGACTGTCAGTAGAGGAAGATGGG

Alignment

ORF - retro_ecab_980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.56 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QTRLKSPEGMSLAEFLYQVLQAYDFYYLFQ-RYGCRVQL-GGSDQLGNIMSGYEFIHKLTGED-VFGITV
          QTRLK.P..MS.A.F.YQV.QA.DF...FQ..YG..VQL.GG.DQLGNIMS.Y..IHKLT.ED..FGI.V
Retrocopy QTRLKTPRDMS-AKF*YQVPQACDFHHQFQ<EYGWWVQL<GGPDQLGNIMSRYKSIHKLTRED<PFGIPV

Parental  PLITSTTGAKLGKS-AGNAVWLNRDKTSPFELYQFFVRQQDDSVERYLKLFTFLPLPEIDHIMQQHVKEP
          .LITST.GA.LGKS..G.AVW.NRD.TSPFELY.FFVR..DD..ER..KL.TFLPLPE.DH.M..HVKEP
Retrocopy ALITSTAGAELGKS<SGSAVWINRDETSPFELYHFFVREKDDLEER*PKLLTFLPLPELDHVMWLHVKEP

Parental  EKWGPQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIDALEVMSDQELKE-LFKEASFSELVLDPGTSV
          .K.GP.KRLAAEVTKLVHGQEGL.SAK.C.QAL.H...D.LEVMSDQE.KE..FKEASFSELVLDPG.S.
Retrocopy QKQGPRKRLAAEVTKLVHGQEGLASAKMCKQALCHRCTDTLEVMSDQEMKE<VFKEASFSELVLDPGASG

Parental  LDTCRKANAIPDGPRGYRMITEGGVSINHRQVTNPESVLVVGQHILKNGLSLLKIG
          .DTC.KANAIPDGPR.Y..IT.G.VSI.HR.VTNPESVLVVGQHILKNGLS....G
Retrocopy *DTCHKANAIPDGPRRYQVITQGRVSISHR*VTNPESVLVVGQHILKNGLSVEEDG

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	0.06 RPM	3.48 RPM
SRP021940_cerebellum	0.00 RPM	7.22 RPM
SRP021940_embryo	0.00 RPM	11.10 RPM
SRP021940_placental_villous	0.00 RPM	7.12 RPM
SRP021940_synovial_membrane	0.00 RPM	6.09 RPM
SRP021940_testis	0.00 RPM	15.79 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_980 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011140	1 retrocopy	retro_ecab_980 ,
Myotis lucifugus	ENSMLUG00000001614	1 retrocopy	retro_mluc_2612,