RetrogeneDB ID: retro_ecab_438

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:76263489..76264320(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPA1
• Ensembl ID: ENSECAG00000023030
• Aliases: None
• Description: inositol(myo)-1(or 4)-monophosphatase 1 [Source:HGNC Symbol;Acc:6050]

Sequence

>retro_ecab_438
ATGGCTGGTCCTTGGCAGGAATGCATGGATTATGCAGTAACACTAGCAAGACAAGCTGGAGAGGTGGTTCGTGACGCCCT
GAAAAATGAAATGAATGTTATGATTAAAAGTTCTCCAACTGATTTGGTAACTGCTACTGACCAAAAAGTTGAAAAAATGC
CTATCTCTTCTATAAAGGAAAAATACCCTTCTCACAGTTTCATTGGTGAGGAATCTGTGGCAGCTGGGGAAAAAAGTGTC
TTAACCGACAACCCTACATGGATCATTGACCCTATCTATGGGACAACCAGCTTTGTACATAGATTTCCTTTTGTAGCTGT
TTTGATTGACTTTGTTGTAAATAAAAAGATGGAATTTGGGGTTGTGTACAGTTGTGTGGAATATAAGATGTACACCGGCA
GGAAGGGAAAAGGTGCCTTCTGTAACAGTCAAAAACTGCAGGTTTCACAACAAGAAGATATTACCAAATCACGCTTGGTG
ACAGAGTTGGGGCCTTCAGGAACACCGGAGACTGTAAGTATTATTCTTTCTAATATGGAAAAGCTTCTTTGCATTCCCAT
TCATGGGATCTGAGGGGTTGGGACAGCAGCTGTTAATATGTGCCTTGTGGCAGCTGGAGCTGTGGATGCGTATTATGAAA
TGGGAGTTCACTGCTGGGACATGGCAGGAGCTGGCATCATTGTTACCGAAGCTGGTGGAGTACTCATGGATGTAATCGGT
GGTCCATTTGGTTTGATGTCACGAAGAATAATTGCTGCAAGTAGTGAAAGTTTAGCAGAAAGGCTAGCCAAAGAAATTCA
GATATTATCTTTTCAAAGAGACGATGAAGAT

Alignment

ORF - retro_ecab_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADPWQECMDYAVTLARRAGEVVRDALKNEMNVMIKSSPADLVTATDQKVEKMLISSIKEKYPSHSFIGE
          MA.PWQECMDYAVTLAR.AGEVVRDALKNEMNVMIKSSP.DLVTATDQKVEKM.ISSIKEKYPSHSFIGE
Retrocopy MAGPWQECMDYAVTLARQAGEVVRDALKNEMNVMIKSSPTDLVTATDQKVEKMPISSIKEKYPSHSFIGE

Parental  ESVAAGEKSVLTDNPTWIIDPIDGTTNFVHRFPFVAVSIGFVVNKKMEFGVVYSCMEDKMYTGRKGKGAF
          ESVAAGEKSVLTDNPTWIIDPI.GTT.FVHRFPFVAV.I.FVVNKKMEFGVVYSC.E.KMYTGRKGKGAF
Retrocopy ESVAAGEKSVLTDNPTWIIDPIYGTTSFVHRFPFVAVLIDFVVNKKMEFGVVYSCVEYKMYTGRKGKGAF

Parental  CNGQKLQVSRQEDITKSLLVTELGSSRTPETVRIVLSNMEKLLCIPIHGIRGVGTAAVNMCLVAAGVADA
          CN.QKLQVS.QEDITKS.LVTELG.S.TPETV.I.LSNMEKLLCIPIHGI.GVGTAAVNMCLVAAG..DA
Retrocopy CNSQKLQVSQQEDITKSRLVTELGPSGTPETVSIILSNMEKLLCIPIHGI*GVGTAAVNMCLVAAGAVDA

Parental  YYEMGIHCWDMAGAGIIVTEAGGVLMDVTGGPFDLMSRRIIAASSKTLAERIAKEIQILPFQRDDED
          YYEMG.HCWDMAGAGIIVTEAGGVLMDV.GGPF.LMSRRIIAASS..LAER.AKEIQIL.FQRDDED
Retrocopy YYEMGVHCWDMAGAGIIVTEAGGVLMDVIGGPFGLMSRRIIAASSESLAERLAKEIQILSFQRDDED

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	2.83 RPM
SRP021940_cerebellum	0.05 RPM	10.75 RPM
SRP021940_embryo	0.03 RPM	11.64 RPM
SRP021940_placental_villous	0.00 RPM	6.88 RPM
SRP021940_synovial_membrane	0.00 RPM	7.77 RPM
SRP021940_testis	0.00 RPM	9.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_438 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_438 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	ENSECAG00000023030	1 retrocopy	retro_ecab_438 ,
Macaca mulatta	ENSMMUG00000002628	1 retrocopy	retro_mmul_467,
Monodelphis domestica	ENSMODG00000006271	1 retrocopy	retro_mdom_1310,