RetrogeneDB ID: retro_ecab_389

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:5108466..5109259(+)
• Located in intron of: ENSECAG00000000407

Retrocopy information

• Ensembl ID: ENSECAG00000014432
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSECAG00000023592
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_ecab_389
ACGAAGGTTTTGGGAACAGTAAAATGGTTCAACGTAAGAAACGGATATGGCTTCATCAAGAGGAATGACACCACGGAAGA
TGTATTTGTACACCACACTGCCATAAAGAATAACCCCAGGAAGCACCTTCGCAGTATAGGAGATGGAGAGACACTGGAGT
TTGATGTTATTGAAGGAGAAAAGGGTGCGGAGGCAGCAAGTTACAGGCCCTGGGGGGGTTCCAGAGCAAGGCAGTAAATA
CGCAGCAGACCTGAACCATTATAGACGCTATCCACGTCGCAGGGGTCCTCCACGCAACTACCAGCAGAATTACCAGAATA
GTGAGAGTGGGGAAAAGAATGAGGGCTCGGAGAGTGCTCCCGAAGGCCAGGCCCAACAGCGGCGGCCCTACCACAGGCAA
CGGTTCCCACCTTACTACATGCGGAGACCCTATTGGCGTCGACCACAGTATTCCAACCCTCCCATGCAAGAAGTGATGGA
GGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACGAGTGAGGCAGAATATGTATTGGGGTTATAGACCACGATTCC
GCAGGGGCCCTCCTGGCCAAAGACAGCCCAGAGAGGCTGGCAATGAAGATAAGGAAAATCAAGGAGATGAGACCCAAGGT
CAGCAGCCACCTCAACGTCGGTACCACCGCAACTTCAATTACCGACACAGACACCCAGAAAACCCTAAACCACAAGATGG
CAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAACTCGTCCACTCCCAAGGCTGAGCAGGGCCAAGATGAG

Alignment

ORF - retro_ecab_389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.41 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGE-KGAEAAN-
          TKVLGTVKWFNVRNGYGFI.RNDT.EDVFVH.TAIK.NNPRK.LRS.GDGET.EFDV.EGE.KG......
Retrocopy TKVLGTVKWFNVRNGYGFIKRNDTTEDVFVHHTAIK-NNPRKHLRSIGDGETLEFDVIEGE<KGCGGSK<

Parental  VTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFP
          VTGPGGVP.QGSKYAAD.NHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPY.R.RFP
Retrocopy VTGPGGVPEQGSKYAADLNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYHRQRFP

Parental  PYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDK
          PYYMRRPY.RRPQYSNPP.Q.EVMEGADNQGAGEQGR.VRQNMY.GYRPRFRRGPP.QRQPRE.GN.EDK
Retrocopy PYYMRRPYWRRPQYSNPPMQ-EVMEGADNQGAGEQGRRVRQNMYWGYRPRFRRGPPGQRQPREAGN-EDK

Parental  ENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE
          ENQGDETQGQQPPQRRY.RNFNYR.R.PENPKPQDGKETKAADPPAENSS.P.AEQG..E
Retrocopy ENQGDETQGQQPPQRRYHRNFNYRHRHPENPKPQDGKETKAADPPAENSSTPKAEQGQDE

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	0.06 RPM	10.92 RPM
SRP021940_cerebellum	0.00 RPM	7.69 RPM
SRP021940_embryo	0.33 RPM	26.72 RPM
SRP021940_placental_villous	0.14 RPM	9.77 RPM
SRP021940_synovial_membrane	0.11 RPM	16.99 RPM
SRP021940_testis	1.92 RPM	67.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_389 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023592	20 retrocopies	retro_ecab_194, retro_ecab_228, retro_ecab_324, retro_ecab_389 , retro_ecab_461, retro_ecab_538, retro_ecab_539, retro_ecab_712, retro_ecab_736, retro_ecab_756, retro_ecab_950, retro_ecab_963, retro_ecab_964, retro_ecab_965, retro_ecab_966, retro_ecab_982, retro_ecab_983, retro_ecab_984, retro_ecab_985, retro_ecab_992,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,