RetrogeneDB ID: retro_ecab_1028

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:56576223..56576831(-)
• Located in intron of: ENSECAG00000003727

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSECAG00000003600
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_ecab_1028
ACGACCAAGTCAGAGCTGCTCAGGCAGTTCCAGCAGCACTAGGAAGATTCAAAGACGCAGAAAGATGGAGAAAGACGTAA
AATTAGTTTTGGTAACATACTATCAGATATGAAAGTTGCCGGATCTGCTACAGTTAGAGTTTGTGCAAGACCAGTGCATC
AGATTTAGTTTAACAAAGGATCTGACAATGATCACAGCCAAGAGAAGACTGCTGATATTAGAAAACATCATAGGAAAAAT
ATACTCAAAGGGAAGAGACTCCATATTTTTGAGAGTAAGGCAGTTACTGAAGAAGCACCTGAAACAGAGACATCACCTTC
ACTTGGGGTGTGGAATTCACTAAGCAGCTAGCCTCAGTAAATTCACAGCCCTTTCAAAATGGTTTTGAAGAGATGATCCA
GTGGAGACATGAGGGGAAACTATGGGAGTTCCCAGTTAACAATGAAGCAGATTTTGATGAGGATGATTCAGGATTTCATG
AATATATATTTCTAGATAAATACTTGGAGAATTTTCCAAAGCAAGAACCAGTTCTCCACTTCATGGAAATGGTGACCTGT
GGTCTTTCCAAAAACCCATATCTGAGTGTTAAACAGAAAGTCAATCAC

Alignment

ORF - retro_ecab_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTKSELLRQLRQHEEDSRAQKEGERPKISFSNIISDMKVAKSATARVSTRPVHQIQFDEGSDDYGGQEKT
          TTKSELLRQ..QH.EDS..QK.GER.KISF.NI.SDMKVA.SAT.RV..RPVHQI.F..GSD....QEKT
Retrocopy TTKSELLRQFQQH*EDSKTQKDGERRKISFGNILSDMKVAGSATVRVCARPVHQI*FNKGSDNDHSQEKT

Parental  ADLRK--RKNIFKGKRLNIFDLKAVTEEAPEAETAPSL-WDVEFAKQLAAVNEQPFQNGFEEMIQWTKEG
          AD.RK..RKNI.KGKRL.IF..KAVTEEAPE.ET.PSL.W.VEF.KQLA.VN.QPFQNGFEEMIQW..EG
Retrocopy ADIRKHHRKNILKGKRLHIFESKAVTEEAPETETSPSL<WGVEFTKQLASVNSQPFQNGFEEMIQWRHEG

Parental  KLWEFPINNEAGFDDDGSEFYEHVFLDKYLEDFPKQGPIRHFMELVTCGLSKNPYLSVKQKVEH
          KLWEFP.NNEA.FD.D.S.F.E..FLDKYLE.FPKQ.P..HFME.VTCGLSKNPYLSVKQKV.H
Retrocopy KLWEFPVNNEADFDEDDSGFHEYIFLDKYLENFPKQEPVLHFMEMVTCGLSKNPYLSVKQKVNH

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	6.02 RPM
SRP021940_cerebellum	0.00 RPM	7.17 RPM
SRP021940_embryo	0.00 RPM	11.99 RPM
SRP021940_placental_villous	0.00 RPM	8.47 RPM
SRP021940_synovial_membrane	0.00 RPM	5.00 RPM
SRP021940_testis	0.00 RPM	15.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1028 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028 ,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,