RetrogeneDB ID: retro_ecab_1009

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:44871940..44872277(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSECAG00000017024
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_ecab_1009
CTGTTCCTAGCAAATTCTGGGGACAACCTTTTAGAGCTGGTGAAATAGTTGTTTTTAAAGTTGAAGGATGAGACATTCCA
GTAGTTCACAGAGTAATCAAAGTTTATGAAAAAGATAATGGAGACAAAAAATTTCTGACTAAGGGAGATAATAATAAAGC
TGACGAAAGAGGCTAGTACAAAGAAGTCCAGAACTGGCTCAAAAAGGATAGGTGGGAAGAGCCAGAGGGTTTTTACCATA
TGCTGCTATGGTCACGATGATAATGAATGACTACCCAAAATTCAATTATGGTCTTTTGGCTGTAATGGATGCATATGTGT
TACTAAAATGTAAATCC

Alignment

ORF - retro_ecab_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 59.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFLTN-FREDPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYKEGQNWLEK
          LFL.N.F...P.RAGEIVVFKVEG.DIP.VHRVIKV.EKDNGD.KFLTKGDNN..D.RG.YKE.QNWL.K
Retrocopy LFLAN<FWGQPFRAGEIVVFKVEG*DIPVVHRVIKVYEKDNGDKKFLTKGDNNKADERG*YKEVQNWL-K

Parental  KDVVGRARGF-LPYVGMVTIIMNDYPKFKYALLAVMGAYVLLKRES
          KD......GF.LPY..MVT.IMNDYPKF.Y.LLAVM.AYVLLK..S
Retrocopy KDRWEEPEGF<LPYAAMVTMIMNDYPKFNYGLLAVMDAYVLLKCKS

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	21.84 RPM
SRP021940_cerebellum	0.00 RPM	24.10 RPM
SRP021940_embryo	0.00 RPM	14.30 RPM
SRP021940_placental_villous	0.00 RPM	29.20 RPM
SRP021940_synovial_membrane	0.00 RPM	12.11 RPM
SRP021940_testis	0.00 RPM	25.71 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1009 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1009 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_775

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009 , retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,