RetrogeneDB ID: retro_ecab_404

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:2767903..2768311(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME2
• Ensembl ID: ENSECAG00000021658
• Aliases: None
• Description: nucleoside diphosphate kinase B [Source:RefSeq peptide;Acc:NP_001191672]

Sequence

>retro_ecab_404
CAGCAGGAGCAGACCATGGCCAACAGTGAGGGTATCTTCATTGCCAGTAAGTTTGATCAGGTCCAGGGGCGCCTCATGGG
AGAGATTCTCAAGCATTTTCAGCAGAAGGATTCCAACTTATTGGTTTGAAATTCATGCAGGCTTCTGAAGATGTTCTCAA
GCAACACTACGTCATCCTGAAGGATGGTCTGTTTTTTGCCAACCTGGTCAAAGACATGTACACAGGGCCAGTGGTTGTCA
TGAGATGAGAGGGGCTGAATGTTGTGAAGACATGCTGGATCATGCTAAGGGAAACCTATCTGTGGGCTTTAAGCTTAGGA
CCATCTTTAGGGATGTTTGCATTCAAGTAGACAGGAACATTATTTATGGCAGCAATTCCTGCAGAGCGCAGAGAAGACTG
GCTTGTGG

Alignment

ORF - retro_ecab_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 60.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QVGRTMANVERTFIAIKPDGVQRSLVGEIIKRFEQK-GFRLVAMKLLQASEDLLKQHYVDLKDRPFFPGL
          Q...TMAN.E..FIA.K.D.VQ..L.GEI.K.F.QK.GF.L...K..QASED.LKQHYV.LKD..FF..L
Retrocopy QQEQTMANSEGIFIASKFDQVQGRLMGEILKHFQQK<GFQLIGLKFMQASEDVLKQHYVILKDGLFFANL

Parental  VKYMHSGPIVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDF-CIQVGRNIIHGSDS-VKSAEKEISL
          VK.M..GP.V.M..EGLNVVKT...ML.ET.......G...G.F.CIQV.RNII.GS.S...SAEK...L
Retrocopy VKDMYTGPVVVMR*EGLNVVKTCWIMLRETYLWALSLGPSLGMF<CIQVDRNIIYGSNS<LQSAEK-TGL

Parental  W
          W
Retrocopy W

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	51.53 RPM
SRP021940_cerebellum	0.00 RPM	71.20 RPM
SRP021940_embryo	0.05 RPM	104.67 RPM
SRP021940_placental_villous	0.00 RPM	89.53 RPM
SRP021940_synovial_membrane	0.00 RPM	135.26 RPM
SRP021940_testis	0.00 RPM	48.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_404 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_404 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404 ,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,