RetrogeneDB ID: retro_ecab_465

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:55825384..55826006(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSECAG00000016651
• Aliases: None
• Description: non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]

Sequence

>retro_ecab_465
AATCTGCTACCAGTTGAAGAATTCTTCATGGTGAAGATACTTGTGATTTCAAATTCGTAGTCTATGACTCCAGTGCAATA
TCAGAACATGCCTTTAGTACAACCCACATATTACATGTCCTGTTGGATTCAACACAGTAAGAATTCCTTGCATCGATGCC
ATGAACTGATCATTCAACAAAAGTTCCTGTTATGTAAGAGGAGGAGGCAATGTCTGCATGTTAGGAAGAATGAAACAATC
TCATCAAGAAGCAAAACAAAAAGAAGTAGAAATAATCTTGGAATTTTTAAAAACATATTTTTAAGAAGACCCTAAAACTC
CTTTGTCCTTCCATGACTTTGTGGCTGATCCACATTTTTTCCATGCACTTTGAAAACCAAATTCATTATATTCCTTCATT
ATGAAAAATGGTTTTGCAAGAAGAAGTCATGACCAAAACAAACTTCTAATAAAAAGTCTTGTTAATATTAACTAACAAAG
CAAGAAAGTTGACTTAAACATCAAAACTAGGAATCAAGAAATTATAGCTTTGAGTTATTGAGACTGGAAGGAAATTGTGA
AGATTTTTGAAATTTCGCTCCCTGCAATCACTTCAAATCAAAGTCAGCAAAGACTAACTTCT

Alignment

ORF - retro_ecab_465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.24 %
• Parental protein coverage: 73.61 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NPLEAEE-LIRDEDSSDFEFIVYDSWKISGKTAENTFNKTHTFHFLLGSIQGEFPVPKPRTDRPRKVPMI
          N.L..EE.....ED..DF.F.VYDS..IS....E..F..TH..H.LL.S.Q.EF....P.TD...KVP..
Retrocopy NLLPVEE<ILHGEDTCDFKFVVYDSSAIS----EHAFSTTHILHVLLDSTQ*EFLASMP*TDHSTKVPVM

Parental  EQRREMPA-QLKRMEESHQEATEKEVERILGLLQTYFREDPDTPMSFFDFVIDPHSF-PRTVENIFHV-S
          .....M.A..L.RM..SHQEA..KEVE.IL..L.TYF.EDP.TP.SF.DFV.DPH.F.P.T....F...S
Retrocopy *EEEAMSA<MLGRMKQSHQEAKQKEVEIILEFLKTYF*EDPKTPLSFHDFVADPHFF<PCTLKTKFII>S

Parental  FIIRDGFARIRLDQDRLPIIEPVNINEESEGIDQNTQIRNQGIIALSYRDWEEIVKTFEISEPVIASGQS
          FI...GFAR...DQ..L.I...VNIN..S...D.N...RNQ.IIALSY.DW.EIVK.FEIS.P.I.S.QS
Retrocopy FIMKNGFARRSHDQNKLLIKSLVNIN*QSKKVDLNIKTRNQEIIALSY*DWKEIVKIFEISLPAITSNQS

Parental  QQRLSA
          QQRL..
Retrocopy QQRLTS

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	3.95 RPM
SRP021940_cerebellum	0.00 RPM	5.97 RPM
SRP021940_embryo	0.00 RPM	15.27 RPM
SRP021940_placental_villous	0.00 RPM	8.37 RPM
SRP021940_synovial_membrane	0.00 RPM	7.30 RPM
SRP021940_testis	0.00 RPM	30.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_465 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_465 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_465 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465 ,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,