RetrogeneDB ID: retro_sara_718

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_28062:529..1519(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSSARG00000011232
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_sara_718
GTCCCAGCCTTCGAGGGTGATGAGGGCTTCTGTGTGTTTGAGAGCAACGCCATTGCCTACTACGTACGTGAGCAACGAGG
AGCTGCGGGGCAGCACCCCCGAGGACGCAGCGCAGGTGGTGTGCAGTGGGTGAGCTTTGCCGACAGCGACAGCGTGCCCC
CGGCTAGTACCTGGGTGTTCCCCACCTTGGGCATCATGCACCACAACAAGCAGGCCACAGAGGATGCGAAGGAGGAGGTG
AAGCGGATTCTGGGGCTGCTGGACGCGCACCCGAAGACGAGGACTTTCCTGGTAGGCGAGCGCGTGACCCTGGCCGACAT
CACAGTTGTCTGCACCCTGCTGTGGCTCTACAAACAGGTTCTGGAGTCTTCTTTCCGCCAGTCCTTCCCCAGTACCAACC
GCTGGTTCCTCACCTGCATCAACCAGCCCCAGTTCCGGATGGTCTTGGGGGAGCTGAAGCTCCGTGGGAAGATGGCCCAG
TTCGACGCCAGACGTTTGCCGAGAGCCAGCCCAAGGAGGAGACTCCACGGAAGGAGAAGGGTTCCCGGGAGGAGAAGCAC
AAGCCCCAGGCCGAGCGGAAGGAGGAGAAGGAGGCAGCCGCCCCTGCTCCTGAGGATGAGATGGACGAGTGTGAGCAGGC
CCTGGCTGCAGAGCCGAAGGCCAAGGGCCCTTTAGCTCACCTGCCCAAGAGCACCTTCGTGTTGGACGAATTCAAACGCG
AGTACTCCAAGGAGGACACGCTGTCGGTGGCGCTGCCGTACTTCTGGGAGCACTTGGACAAGGACAGCTGGTCCCTGTGG
TTCTCCGAGTACTGCTTCCCCGAGGAGCTCACCCAGACCTTCACGAGCTGCAACCTCATCACAGGGATGTTCCGGCGACT
GGACAAGCTGAGGAAGAACGCCTTCGCCCAGTGTCATCCTCTTCGGAACCAACAGCAGCAGCTCCATTTCTGGCATCTGG
GTCTTCCGCGGCCAGGAGCTGGCCTTTCCG

Alignment

ORF - retro_sara_718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPAFEGDDGFCVFESNAIAYYVSNEE-LRGSTPEA-AAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNK
          VPAFEGD.GFCVFESNAIAYYV.......G..P....A..VQWVSFADSD.VPPASTWVFPTLGIMHHNK
Retrocopy VPAFEGDEGFCVFESNAIAYYVREQRGAAGQHPRGRSAGGVQWVSFADSDSVPPASTWVFPTLGIMHHNK

Parental  QATENAKEEVKRILGLLDAHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQSFPNTNRWFLTCI
          QATE.AKEEVKRILGLLDAH.KTRTFLVGERVTLADITVVCTLLWLYKQVLE.SFRQSFP.TNRWFLTCI
Retrocopy QATEDAKEEVKRILGLLDAHPKTRTFLVGERVTLADITVVCTLLWLYKQVLESSFRQSFPSTNRWFLTCI

Parental  NQPQFRTVLGEVKLCEKMAQFDAKK-FAESQPKKETPRKEKGSREEKQKPQAERKEEKKAAAPAPEDEMD
          NQPQFR.VLGE.KL..KMAQFDA...FAESQPK.ETPRKEKGSREEK.KPQAERKEEK.AAAPAPEDEMD
Retrocopy NQPQFRMVLGELKLRGKMAQFDARR<FAESQPKEETPRKEKGSREEKHKPQAERKEEKEAAAPAPEDEMD

Parental  ECEQALAAEPKAKDPFAHLPKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWFSEYRFPEELTQ
          ECEQALAAEPKAK.P.AHLPKSTFVLDEFKR.YS.EDTLSVALPYFWEH.DKD.WSLWFSEY.FPEELTQ
Retrocopy ECEQALAAEPKAKGPLAHLPKSTFVLDEFKREYSKEDTLSVALPYFWEHLDKDSWSLWFSEYCFPEELTQ

Parental  TFMSCNLITGMFQRLDKLRKNAFA-SVILFGTN-SSSISGIWVFRGQELAFP
          TF.SCNLITGMF.RLDKLRKNAFA.SVILFGTN.SSSISGIWVFRGQELAFP
Retrocopy TFTSCNLITGMFRRLDKLRKNAFA>SVILFGTNSSSSISGIWVFRGQELAFP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_718 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus	ENSSARG00000011232	1 retrocopy	retro_sara_718 ,