RetrogeneDB ID: retro_ecab_134

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:73664828..73665291(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSECAG00000004925
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_ecab_134
AGGTCCTCCTGAAGGGTCATCTGGAGCAGCAAGAGGAAAACTGTCACTCCTTAGAAGAAGCTGAAACTATGATAAGGACT
ACCATCAGAAGAAAGTGTAGTCTGAACTGAGATCCATCGGTGCCCTAATCCTGGAATTGTTGGATAATTATTAACAGTCA
ATGCAACCAATCCAGAGAGTAAGGTCTTCAGTCTGAAAATGAAAGGGATCACTTCCAGGACCTTGCTGACGTTGCATGTG
GTGAGGATCAAAAACAAATGATAGATAATTCCCAAGGAATTTAGCAACAAACATTTGATATAAACCAGAAAGAGATGCAA
CTCACACACACAGTCCACCTGGGGCTGGCTCCTCACTCTTTTGTGTTTTGCTAGGAACTCCTTAATAACCCGGAGCTTGC
TATACACTGACTAAAACAGCTTTTGATGAGGCCATCATAGAACTTGATGCACTGAACAAAGAC

Alignment

ORF - retro_ecab_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.78 %
• Parental protein coverage: 62.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RSAWRVISSIEQKTDTSDKKLQL-IKDYREK-VESELRSICTTVLELLDKY-LIANATNPESKVFYLKMK
          RS..RVI.S...KT.T..KKL.L..KDY..K.V.SELRSI....LELLD.Y.L..NATNPESKVF.LKMK
Retrocopy RSS*RVIWSSKRKTVTP*KKLKL>DKDYHQKKV*SELRSIGALILELLDNY<LTVNATNPESKVFSLKMK

Parental  G-DYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELAC-T
          G.D.F..LA.VACG.D.KQ.IDNSQG..Q..FDI..KEMQ.TH...LGLA....VF..E.LNNPELA..T
Retrocopy G<DHFQDLADVACGEDQKQMIDNSQGI*QQTFDINQKEMQLTHTVHLGLAPHSFVFC*ELLNNPELAI<T

Parental  LAKTAFDEAIAELDTLNED
          L.KTAFDEAI.ELD.LN.D
Retrocopy LTKTAFDEAIIELDALNKD

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	69.30 RPM
SRP021940_cerebellum	0.00 RPM	292.33 RPM
SRP021940_embryo	0.00 RPM	229.28 RPM
SRP021940_placental_villous	0.00 RPM	141.93 RPM
SRP021940_synovial_membrane	0.00 RPM	93.50 RPM
SRP021940_testis	0.00 RPM	133.32 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_134 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_134 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000004925	1 retrocopy	retro_ecab_134 ,
Equus caballus	ENSECAG00000021882	3 retrocopies	retro_ecab_202, retro_ecab_31, retro_ecab_624,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Otolemur garnettii	ENSOGAG00000000547	3 retrocopies	retro_ogar_1047, retro_ogar_1732, retro_ogar_39,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,
Tursiops truncatus	ENSTTRG00000000871	4 retrocopies	retro_ttru_1006, retro_ttru_1109, retro_ttru_1530, retro_ttru_1536,