RetrogeneDB ID: retro_ecab_340

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:84311225..84311670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYPL1
• Ensembl ID: ENSECAG00000009695
• Aliases: None
• Description: synaptophysin-like 1 [Source:HGNC Symbol;Acc:11507]

Sequence

>retro_ecab_340
GAATATTCTTTTTCTGCGTAATTCAGTGTCACCTTTGAGGCCTAGTTTTCCTCTCCTGCATCACTGTGCTTGTGCTTTAT
ATTGGTCAATTGACCTTATATTGGGGAGAGCGGAAAACTTTCCACAACTGACCTTGATATTTTCATTGCTACTTTTTTAA
GGTTGACAAGAATTTCATCTTGTGCCACAGCTCTCACAGATATCGAAACAGCCATGGGTGAAAACATTGTTCAGAATTTC
TACCTTGTTAGCAGTAAAGAATAATGGTTCATTTGGCTCTATCTCTATTACTTCTCTAAATGTAACTGTAATTTTTGACT
TTGTGAATATGATATCTTCAGGAGGAAATGCTTGGTTTGTATATATAGAATCAAATATATTACACAGACCATCAAATGAG
ACCACTGCCCAAGGTCAAATATGTATTTTACCTTCTACAGGAATA

Alignment

ORF - retro_ecab_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.65 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DYSSSAQFYVTFAV-FVFLYCMAALLLYLGYTSLY-RDSRKLTMTDFVITLVATFLWLVSTSAWAKALTD
          .YS.SA.F.VTF....VFL.C...L.LY.G...LY...S.KL..TD..I...ATFL.L...S..A.ALTD
Retrocopy EYSFSA*FSVTFEA<LVFLSCITVLVLYIGQLTLY>GESGKLSTTDLDI-FIATFLRLTRISSCATALTD

Parental  IKIATGPNIVR-ELGPCNQ-RVTCHFSVT-SMGSLNVSVIFGFLNMILWGGNAWFVYKETS-LHSPSNTS
          I..A.G.NIV..E..PC.Q.R...H.....S..SLNV.VIF.F.NMI..GGNAWFVY.E...LH.PSN..
Retrocopy IETAMGENIVQ<EFLPC*Q*RIMVHLALS<SITSLNVTVIFDFVNMISSGGNAWFVYIESNILHRPSNET

Parental  ASHGQGGVPPPSGI
          ...GQ....P..GI
Retrocopy TAQGQICILPSTGI

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	19.95 RPM
SRP021940_cerebellum	0.00 RPM	21.29 RPM
SRP021940_embryo	0.00 RPM	27.16 RPM
SRP021940_placental_villous	0.00 RPM	72.02 RPM
SRP021940_synovial_membrane	0.00 RPM	51.69 RPM
SRP021940_testis	0.00 RPM	250.40 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_340 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016176	2 retrocopies	retro_cjac_1588, retro_cjac_2483,
Cavia porcellus	ENSCPOG00000009221	1 retrocopy	retro_cpor_239,
Equus caballus	ENSECAG00000009695	1 retrocopy	retro_ecab_340 ,
Homo sapiens	ENSG00000008282	1 retrocopy	retro_hsap_1817,
Gorilla gorilla	ENSGGOG00000006497	1 retrocopy	retro_ggor_1984,
Myotis lucifugus	ENSMLUG00000014980	3 retrocopies	retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta	ENSMMUG00000019593	2 retrocopies	retro_mmul_1251, retro_mmul_1464,
Mus musculus	ENSMUSG00000020570	1 retrocopy	retro_mmus_3470,
Nomascus leucogenys	ENSNLEG00000008861	1 retrocopy	retro_nleu_2720,
Oryctolagus cuniculus	ENSOCUG00000015127	3 retrocopies	retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii	ENSOGAG00000008079	2 retrocopies	retro_ogar_1970, retro_ogar_2520,
Ochotona princeps	ENSOPRG00000006755	2 retrocopies	retro_opri_210, retro_opri_448,
Pongo abelii	ENSPPYG00000018292	1 retrocopy	retro_pabe_2370,
Pan troglodytes	ENSPTRG00000019570	2 retrocopies	retro_ptro_1173, retro_ptro_1939,
Rattus norvegicus	ENSRNOG00000009856	2 retrocopies	retro_rnor_2273, retro_rnor_2992,
Sorex araneus	ENSSARG00000013935	1 retrocopy	retro_sara_450,
Ictidomys tridecemlineatus	ENSSTOG00000020871	1 retrocopy	retro_itri_1243,
Tupaia belangeri	ENSTBEG00000009095	2 retrocopies	retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta	ENSTSYG00000013296	2 retrocopies	retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus	ENSTTRG00000002848	1 retrocopy	retro_ttru_661,