RetrogeneDB ID: retro_ecab_299

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:65274505..65275163(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG4
• Ensembl ID: ENSECAG00000012564
• Aliases: None
• Description: B-cell translocation gene 4 [Source:HGNC Symbol;Acc:13862]

Sequence

>retro_ecab_299
GATGAAATTGCAACAACAGTTTTCTTTGTTACGAGATTAGTGAAAAAACATAAGTTGAGTAAACAGCAAATAGAAGACTT
TGTAAAACAGTTGATGACAAACTTGTTTGAAACATACAGAAGTCACTGGTACTCTGGTTACCTTTCTAATGGGCAAGGCT
TCAGGTATATCGGGATAAACCATTAGAATAAAGATCACATCCTAGAAAGGGCTCATGCTGAAAGTGAAGTGGATTTTTCT
CACCCTAGACTTCCGAAGGAGAGGAGCATTTAGGTAGATCACTTTGAAGTTTGCTATAGGTATGGTGAGAAAAATCATCT
ATTTACAGTTCTTCTTTTAAAGGCAGATGGGAGGAATGAGGACTCTCCCAGCAAATCAGTTATGTTCTTGGTAGAGCCAG
ATTAGACTGCTCCTCTGCCACTTCCTTCAGTGAAGAAAGTTGTAACAAAGAACCTCAGATAATTCCTGAAGTCAGCAATC
CAAAGAGTATTTGTCAGATTGAAAACTTGAAACGACTCTTTTAATATTGGTTCCAAATCACCCACAAAAAGAATATGGTG
ATGGCCATATGGGCATCCTAGGGAATGTTTATCAAGTGTTGTATAAGAACCCTGAGGGTCATAGGCCTGTTGCTATACAC
AGGGTGGGCAGGTACCAC

Alignment

ORF - retro_ecab_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 82.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEIATTVFFVTRLVRKHDRLSKQQIEDFAEKLITILFETYRSHWHSDCPSKGQAFRCIRINNNQNKDPIL
          DEIATTVFFVTRLV.KH..LSKQQIEDF...L.T.LFETYRSHW.S...S.GQ.FR.I.IN...NKD.IL
Retrocopy DEIATTVFFVTRLVKKH-KLSKQQIEDFVKQLMTNLFETYRSHWYSGYLSNGQGFRYIGINH*-NKDHIL

Parental  ERACAESNVDFSHLGLPKEMTIWVDPFEVCCRYGEKNHPFTI-ASFKGRWEERELSQQISYAVSRATLDS
          ERA.AES.VDFSH..LPKE..I.VD.FEVC.RYGEKNH.FT...SFKGRWEE..LSQQISY...RA.LD.
Retrocopy ERAHAESEVDFSHPRLPKERSI*VDHFEVCYRYGEKNHLFTV<SSFKGRWEE*GLSQQISYVLGRARLDC

Parental  SPGSSSDEEGCNQEPQIIPKVNNPKSIYQVENLKRPFQSWFQIPRKNNMV-DGRMGLLENAYHVLHKNPK
          S...S..EE.CN.EPQIIP.V.NPKSI.Q.ENLKR.F..WFQI..K.NMV.DG.MG.L.N.Y.VL.KNP.
Retrocopy SSATSFSEESCNKEPQIIPEVSNPKSICQIENLKRLF*YWFQITHKKNMV<DGHMGILGNVYQVLYKNPE

Parental  GHRAAAIHTLEFYN
          GHR..AIH....Y.
Retrocopy GHRPVAIHRVGRYH

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_299 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_299 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1324
Sus scrofa	retro_sscr_680

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014210	2 retrocopies	retro_cfam_1324, retro_cfam_471,
Choloepus hoffmanni	ENSCHOG00000000032	1 retrocopy	retro_chof_2674,
Equus caballus	ENSECAG00000012564	1 retrocopy	retro_ecab_299 ,
Monodelphis domestica	ENSMODG00000014496	1 retrocopy	retro_mdom_1647,
Sus scrofa	ENSSSCG00000015020	1 retrocopy	retro_sscr_680,
Tursiops truncatus	ENSTTRG00000010435	1 retrocopy	retro_ttru_1303,