RetrogeneDB ID: retro_ecab_1055

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:24200046..24200784(+)
• Located in intron of: ENSECAG00000020894

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRPT1
• Ensembl ID: ENSECAG00000009917
• Aliases: None
• Description: tRNA phosphotransferase 1 [Source:HGNC Symbol;Acc:20316]

Sequence

>retro_ecab_1055
ATGAACTCCTCTGGCGGAAGGAGGCAGGAAGCAGCAGGGCCTGGGGGCAGAAGTACTCACAGATCCCAAGAATCAGATGT
GCAACTGTCCAAGGCTCTGCCCTGCGCCCTGTGCCACGGGGCCCTGAAGCTGAGGTTTCCCACGGGGGCCAACAGCTTTG
TGCCCCTGGGCGCCCTCCTGCAGCTCCCCAGTTCCGAAGCATCTCAGCTAAAGGTGTGCACTGTGTGGTGGACACCAAAG
GGAAGCAGCGCTTTGCCCTGCAGCTGGGGGACTCCAGCACTGGCCTTCTCATCCAGGCCAATCAGGGACACTCTCTGTAG
GTACCTTAGTTGGAGTTGATGCCCCTGGGGACCCCACAGGCCCTGCCCTGATGCTCATCCATGGCACATTCTGGCAGCAC
TGGCCATCCATCTTGCTCAAGGGCCTGTCCTGCTGGGGAAGGATGCACATCCACCTGGCCCTAGGACTGCCTGGGGATCC
TGGTGTCAGTGGCATGTGGTCAAACTGCAGACGGGTCATGTTCATCAACAGGCCCCTGGCCCTGGCAGATGGAGCCCTTT
TCTTCAGCTCTGCCAATGAAGTGATTCTGACTCCAGGGAAAGCTGATGGCTTCCTGCTTCCCAAGTACTTCAAGGAGGCC
CTGCAGCTATGCCCTACCGAAACCCTCTCTCCTTGGCTGATAATGAAAAGACAGAGTGTCAGAGTGGCCCTGAGCACAGC
TCCAGAGGAAGAAGGATA

Alignment

ORF - retro_ecab_1055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDTSGGRRQEAGGPRGRKARRPREQDRDMQLSKALSYALRHGALKLGLPMGADGFVPLGALLQLP-QFRS
          M..SGGRRQEA.GP.GR...R...Q..D.QLSKAL..AL.HGALKL..P.GA..FVPLGALLQLP.QFRS
Retrocopy MNSSGGRRQEAAGPGGRSTHR--SQESDVQLSKALPCALCHGALKLRFPTGANSFVPLGALLQLP<QFRS

Parental  FSAEDVQRVVATNAKQRFALQPGDPSTGPLIRANQGHSLQVPELELMPLETPQALP-PMLIHGTFWQHWP
          .SA..V..VV.T..KQRFALQ.GD.STG.LI.ANQGHSL.VP.LELMPL.TPQALP..MLIHGTFWQHWP
Retrocopy ISAKGVHCVVDTKGKQRFALQLGDSSTGLLIQANQGHSL*VP*LELMPLGTPQALP<LMLIHGTFWQHWP

Parental  SILLKGLSCRGRTHIHLATGLPGDPGVISGIRPNCEVAVFINGPLALADGIPFFRSANGVILTPGDADGF
          SILLKGLSC.GR.HIHLA.GLPGDPGV.SG...NC....FIN.PLALADG..FF.SAN.VILTPG.ADGF
Retrocopy SILLKGLSCWGRMHIHLALGLPGDPGV-SGMWSNCRRVMFINRPLALADGALFFSSANEVILTPGKADGF

Parental  LFPKYFKEALQLRPT-RKPLSLAGDEETECQSGPKHSSRGRRM
          L.PKYFKEALQL.PT.R.PLSLA..E.TECQSGP.HSSRGRR.
Retrocopy LLPKYFKEALQLCPT<RNPLSLADNEKTECQSGPEHSSRGRRI

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	9.68 RPM
SRP021940_cerebellum	0.00 RPM	14.39 RPM
SRP021940_embryo	0.00 RPM	11.89 RPM
SRP021940_placental_villous	0.00 RPM	6.16 RPM
SRP021940_synovial_membrane	0.05 RPM	9.03 RPM
SRP021940_testis	0.00 RPM	19.31 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1055 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1055 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1055 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009917	1 retrocopy	retro_ecab_1055 ,
Sus scrofa	ENSSSCG00000013040	1 retrocopy	retro_sscr_1146,
Tursiops truncatus	ENSTTRG00000010252	1 retrocopy	retro_ttru_1283,