RetrogeneDB ID: retro_ecab_468

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:4319138..4319635(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B3
• Ensembl ID: ENSECAG00000019885
• Aliases: None
• Description: ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:HGNC Symbol;Acc:806]

Sequence

>retro_ecab_468
GGTTTGATCTTGATCTTGTGCCTAGTGTTTTATGGGTTCCTGGCTGCACTCTTTTCGTTCTAATGTGGGCTACACTTCGG
ACTGTGAACGATGAGGTTCCAAAATATCATGATCAGATTGCTAGTCTAGAATTAGGGCTTTTCAAAAAACAGCGAGTGCC
TTAGAATACATGTTCAGTGTGTCTGACCCAAATTCCTATAAAGGGTACATAGAAGACATTTGAAAGTTTCTAAAGCCATG
TGATTTAGAAGGACAGAAGAAGCACACAGTCTGTCCTGATGCAGCACTTTTTGAACAGAAAAGTCCAATTTATGTTGCAC
GTCAGTCTCCTGTTTTCTTACTTGAAGAATGCAGTGGTGTGCATGATCCTGATTTTGGCTCTTCAAAAAGGAAGCCCTTG
TATTCTTGTAAAAATAAACAGAATAAGTAGATTAAAGCCTCAAGGAAAACTAAGGATAGCAGTGGTTCAAAAATGAAAAT
ACAGCAGTTCTATCAAC

Alignment

ORF - retro_ecab_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.36 %
• Parental protein coverage: 68.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLILLFYLVFYGFLAALFSF-TMWAMLQTLNDEVPKYRDQIPSPGL-MVFPKPVTALDYSFRVSDPESYR
          GLIL...LVFYGFLAALFSF..MWA.L.T.NDEVPKY.DQI.S..L...F.K...AL.Y.F.VSDP.SY.
Retrocopy GLILILCLVFYGFLAALFSF<LMWATLRTVNDEVPKYHDQIASLEL<RAFQKTASALEYMFSVSDPNSYK

Parental  GYVDDLTKFLKSYDLEEQKNLTACPDGALREQKGPTYTACQFPVVSLKGCSGVEDPEFGYST-GNPCILV
          GY..D..KFLK..DLE.QK..T.CPD.AL.EQK.P.Y.A.Q.PV..L..CSGV.DP.FG.S..G.PCILV
Retrocopy GYIEDI*KFLKPCDLEGQKKHTVCPDAALFEQKSPIYVARQSPVFLLEECSGVHDPDFGSSK>GSPCILV

Parental  KMNRIIGLKPQGKPRINCISKGEKTATLS
          K.NRI..LKPQGK.RI....K........
Retrocopy KINRISRLKPQGKLRIAVVQK*KYSSSIN

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	30.58 RPM
SRP021940_cerebellum	0.00 RPM	59.98 RPM
SRP021940_embryo	0.03 RPM	41.27 RPM
SRP021940_placental_villous	0.00 RPM	54.13 RPM
SRP021940_synovial_membrane	0.00 RPM	54.05 RPM
SRP021940_testis	0.00 RPM	58.89 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_468 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468 ,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,