RetrogeneDB ID: retro_ecab_713

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:38370784..38371481(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000009124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3G
• Ensembl ID: ENSECAG00000021436
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit G [Source:HGNC Symbol;Acc:3274]

Sequence

>retro_ecab_713
ATTGTCCACAGCTTCAGAATTGAGATCTAGAAGAGCTCAAAGGCCATTTCAAGGAGGAAGAACTGGAAGAAGTTTGGGAA
CTCAAAGTTTGACCAATGTGGCCACCAGCACAGTCAGTGGTGATGTGCCCGTGACTGTTCATCAAAGAGGATTTGAACTG
CCAGGAGGACCCGATGAACAAGCTCAAGGGCCAGAAGGTTGAGTTCTGCCGCATCTGCAAGGCAACAACTGGAGGACTCG
TTGCCCCACACAAGGATACACTGTGGCCCGTGCAAAAGGAGCTGGCCGAGAAGGTGGGACTGTCCACTGGCAAGAAGGCA
AAGTTGCCCAAACAGTTGGACCCTATGTATACAGCCCAAAACAAGACAGGGAAGTATGTGCCATGAGCCTGCGGGTCAGG
GCCAGCCACTGTGGGAAGTCCACACAGCCCAATCACACAGTTGATGACAATGCCATCATCTTCGTTTCCACCCTGTCAGA
GGACACTCATGATACTGACCTGCAGGAGCTCTTCCAGTCCTTTGGCTCCATCTTATGCATCTACCTGGCAAAGGACAAGA
CCACTGGCCAGTCCAAGGGCTTTGCCGTCATCAGATTTCACAGCTATGAGGACACCTCAAGTGCCCTTGCTGACATGTCC
AGCTGTGGCTGTGACCACCTCATCCTCAGTGTCAAGTGGGTCAAGCCCTCAACCAAC

Alignment

ORF - retro_ecab_713 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.22 %
• Parental protein coverage: 75.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IVRTFRIE-TRKASKAVARRKNWKKFGNSEFDPPGPNVATTTVSDDVSMT-FITSKEDLNCQEEEDPMNK
          IV..FRIE..R.A.............G.........NVAT.TVS.DV..T.FI..KEDLNCQE..DPMNK
Retrocopy IVHSFRIE>SRRAQRPFQGGRTGRSLGTQSLT----NVATSTVSGDVPVT>FI--KEDLNCQE--DPMNK

Parental  LKGQKIVSCRICK-GDHWTTRCP-YKDTLGPMQKELAEQLGLSTGEKEKLPGELEPVQATQNKTGKYVP-
          LKGQK...CRICK.G..W.TRCP..KDTL.P.QKELAE..GLSTG.K.KLP..L.P....QNKTGKYVP.
Retrocopy LKGQKVEFCRICK<GNNWRTRCP>HKDTLWPVQKELAEKVGLSTGKKAKLPKQLDPMYTAQNKTGKYVP<

Parental  PSLRDGASRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI
          .SLR..AS..G.S.QPN...DDNA.I.V..LSEDT..TDLQELF..FGSI..IYLAKDKTTGQSKGFA.I
Retrocopy MSLRVRASHCGKSTQPNHTVDDNAIIFVSTLSEDTHDTDLQELFQSFGSILCIYLAKDKTTGQSKGFAVI

Parental  SFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN
          .FH..ED...A.A..S..G.DHLIL.V.W.KPSTN
Retrocopy RFHSYEDTSSALADMSSCGCDHLILSVKWVKPSTN

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	214.34 RPM
SRP021940_cerebellum	0.00 RPM	120.69 RPM
SRP021940_embryo	0.08 RPM	178.50 RPM
SRP021940_placental_villous	0.00 RPM	112.44 RPM
SRP021940_synovial_membrane	0.05 RPM	190.22 RPM
SRP021940_testis	0.06 RPM	209.73 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_713 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_713 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_713 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021436	1 retrocopy	retro_ecab_713 ,
Myotis lucifugus	ENSMLUG00000014196	1 retrocopy	retro_mluc_2407,
Otolemur garnettii	ENSOGAG00000014463	3 retrocopies	retro_ogar_101, retro_ogar_1577, retro_ogar_1661,
Rattus norvegicus	ENSRNOG00000020619	1 retrocopy	retro_rnor_1731,