RetrogeneDB ID: retro_ecab_839

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:60908345..60908984(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175B
• Ensembl ID: ENSECAG00000023340
• Aliases: None
• Description: family with sequence similarity 175, member B [Source:HGNC Symbol;Acc:28975]

Sequence

>retro_ecab_839
TTTGACAAGCATAGAGTAATGAAAGACACTGAGGTAATTTACAGGTTTATAATACACTTCACCCAGGCAGTGCGTGCAGA
TGTAGAAAAGAATGAGCAAGTTGTTGAATCTTGTCAGGCAGAAGTGAACAAATTAAGAAGACAAATCAATCAGATGAAAT
GGAAAAGAACAAGAAAGACGATTGCAGCAGGCGATGCTAAGCAGACAGATGCTGTATGAAAGTTTGGAACCAGTGGTCAG
TCCTCGGATGCCCTAACTGGGTTTTTAGCTGAAGGTTGAAGTACACTGGGAGATGCAGAGGATTCTGGTCCTCCTCCTTC
TTATTCTGGTTTTTCACTCACACAGTCTGGAAAGTACTTTGAGCCTTTCTCTATGTAAAGTAGTGTCTTTGTACCTTGAC
CTCAAGCCATGGGCTCTTCCAATTATGCTTCCACCAGTGCCGGACTGAAGTATCCCAGAAGTGGAGAAGACTTTCTTCCT
TCCCAAAGAGTAGCTGGAGACAGACTTGAAGAATCAGATAAAAGTGATTACGAAAATTTGATTGATCTTACAGAGCTTTC
TAATAGGGAATACTTACATTCAAGGAATTCAGGATACGTGACATATTCCCATGGGGTCTCCAGGAACACTCAGACCTCA

Alignment

ORF - retro_ecab_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 51.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FDKDGVMKDIRAIYQVYNALQEKVQAVCADVEKSERVVESCQAEVNKLRRQITQRK-NEKEQE-RRLQQA
          FDK..VMKD...I...Y.......QAV.ADVEK.E.VVESCQAEVNKLRRQI.Q.K..EK....RRLQQA
Retrocopy FDKHRVMKDTEVI---YRFIIHFTQAVRADVEKNEQVVESCQAEVNKLRRQINQMK<MEKNKK<RRLQQA

Parental  MLSRQMAPESLEPGFSPRMP-YSGFVAEGRSPLGDAEASDPPPPYSD-FHSNNQESTLSHP-RMETSVFM
          MLSRQM..ESLEP..SPRMP...GF.AEG.S.LGDAE.S.PPP.YS..FHS...ESTLS....M..SVF.
Retrocopy MLSRQMLYESLEPVVSPRMP<LTGFLAEG*STLGDAEDSGPPPSYSG>FHSHSLESTLSLS<SM*SSVFV

Parental  PRPQAVGSSSYASTSAGLKYPGSGADLPPPRRAAADSAEESDDSDYEHLIDPTEPSNSECSHSRDSRPMT
          P.PQA.GSS.YASTSAGLKYP.SG.D..P..R.A.D..EESD.SDYE.LID.TE.SN.E..HSR.S...T
Retrocopy P*PQAMGSSNYASTSAGLKYPRSGEDFLPSQRVAGDRLEESDKSDYENLIDLTELSNREYLHSRNSGYVT

Parental  HPDGGSRNTQTS
          ...G.SRNTQTS
Retrocopy YSHGVSRNTQTS

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	7.73 RPM
SRP021940_cerebellum	0.00 RPM	8.57 RPM
SRP021940_embryo	0.00 RPM	12.25 RPM
SRP021940_placental_villous	0.00 RPM	5.77 RPM
SRP021940_synovial_membrane	0.05 RPM	7.08 RPM
SRP021940_testis	0.00 RPM	8.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_839 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_839 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023840	1 retrocopy	retro_btau_729,
Choloepus hoffmanni	ENSCHOG00000007635	3 retrocopies	retro_chof_1691, retro_chof_2426, retro_chof_2563,
Equus caballus	ENSECAG00000023340	1 retrocopy	retro_ecab_839 ,