RetrogeneDB ID: retro_sara_69

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_1922:442474..443255(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSSARG00000009067
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_sara_69
AAGATAATCAAACATTTTCAAGAAGGAGACAAGGAACGGAGGTGGTTCAAAGTGTGCTTTTGGCCTTGCTGTAGATGATT
GCTTCAAAGTTATCAATTGCTTTCCATTCCTTCAGTACATGGAAGAAGATACTGATTTTGATGATCAGTATCAGATGGAA
ATGATGCAGAGCCTGCACCATGTAAACATTTATCACCTCCACATGGACTGGTATCAGTTCACATACTATGGCTCATTTGT
CACCCAGGCACTTTTGGATTCTCAGTTCAACTACCAGCATGCCATTGAAGAATGTGTCGTTCTCAATTATGCTCCGATTA
AAACTGCCCAAGGGTCTGTCTCACTGAAGGCATACAGAATGACTCATAAACTGATGGAAGTTTGTAAAGAGAAGGATTTT
TCTCCTGAAGCATTGAAAATGGCAAGCATCACCTTTGAGTACATGTTTGAAGAAGTGCCGATTATAATTAAAAATTCACA
TCTGATCAATGTACGAATGTGGGAGTTTGAGAAGAAGTCATCTGTAGTAGAAAAGCATGAATTGCTCAGTTTTGCTAACA
GCAAACATTTGGGGAAAAATCTACAGCTGCTGATGGACAGTGTGGATGATATGAGCCAAGATATAGTTAAATATAACACA
TACATGAGAAAGACGAGTAAACAGCAGCAGTGGAAACATCAGCATCAGCAGTGTTGCCAGCAAGAGAATATGTAGCCACA
GAGTCGAGAGGAAACTCCATTCCCTGAGGAGGATTTGTCCAAACTTTTTAAACGCCCCCAG

Alignment

ORF - retro_sara_69 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 74.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KIIKHYQE-EGQGTEVVQGVLL-GLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHL
          KIIKH.QE...QGTEVVQ.VLL.GL.V.D.....NCFPF.Q..E.D.DFD..QYQMEMM.SL.HVNI.HL
Retrocopy KIIKHFQE<RRQGTEVVQSVLL<GLAVDDCFKVINCFPFLQYMEEDTDFDD-QYQMEMMQSLHHVNIYHL

Parental  HVGWYQSTYYGSFVTRALLDSQFSYQHAIEESVVLNYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPE
          H..WYQ.TYYGSFVT.ALLDSQF.YQHAIEE.VVLNY.PIKTAQGS.SLKAYR.T.KLMEVCKEKDFSPE
Retrocopy HMDWYQFTYYGSFVTQALLDSQFNYQHAIEECVVLNYAPIKTAQGSVSLKAYRMTHKLMEVCKEKDFSPE

Parental  ALKKASITFEYMFEEVPIIIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDDMSQ
          ALK.ASITFEYMFEEVPIIIKNSHLINV.MWE.EKKS.V..KHELLS.A.S.HLGKNLQLLMD.VDDMSQ
Retrocopy ALKMASITFEYMFEEVPIIIKNSHLINVRMWEFEKKSSVVEKHELLSFANSKHLGKNLQLLMDSVDDMSQ

Parental  DIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEEDLSKLFKPPQ
          DIVKYNTYMR.TSKQQQ.KHQ.QQ..QQENM..QSR.E.P.PEEDLSKLFK.PQ
Retrocopy DIVKYNTYMRKTSKQQQWKHQHQQCCQQENM*PQSREETPFPEEDLSKLFKRPQ

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_69 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69 ,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,