RetrogeneDB ID: retro_sara_417

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_196736:7977..8387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSSARG00000011001
• Aliases: None
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24839]

Sequence

>retro_sara_417
CAAAAGAAAGACTTAACTGCTATGTCAGTAAAATAAGTTCTTCAAAGCTTGGTTGGTGATAGTATCATTGGCTACGAGAG
GATTGGAACATCTAATTATTATTGCGCGTTTCTAGTAAAGCTCTTCATGCAAGGAAATGAAAGTTGGAGACTTCTGGAAT
CTCAGTTATCCAAGGGAAACCAAAAGCATGCAAATCTACAAAAAAGTACCAAGAAGACCAAAATGGGCTGACATGACACA
GAAGAAAGAACAATGCTAGATAAAGAGTTTTCTTCACTTTCAAACAAAGGGAACAGCTGAAAACAGAAGTAGAAAAATAA
AGAGATGGTGACCCACAAGTTGTGGAAAAAATATGTCAAGCAAATGATGTAGGCCATGAAACTGCTACCCGGTGGACTGA
TAATATATAT

Alignment

ORF - retro_sara_417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.14 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEKGITAMSVKEVLQSLVDDGMVDCERIGTSNYYWAF-PSKALHARKRKLE-VLESQLSEGNQKHANLQK
          ..K..TAMSVK.VLQSLV.D.....ERIGTSNYY.AF..SKALHARK.KLE..LESQLS.GNQKHANLQK
Retrocopy QKKDLTAMSVK*VLQSLVGDSIIGYERIGTSNYYCAF<SSKALHARK*KLE>LLESQLSKGNQKHANLQK

Parental  SIEKAKIGRHETEERAMLTKELSALR-IPREQLKAEI-KYRECDPQVVEEIRQANEVAKEAANRWTDNIF
          S..K.K.G.H.TEER.ML.KE.S.L....REQLK.E..K.R..DPQVVE.I.QAN.V..E.A.RWTDNI.
Retrocopy STKKTKMG*HDTEERTMLDKEFSSLS<KQREQLKTEVEK*RDGDPQVVEKICQANDVGHETATRWTDNIY

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_417 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417 ,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,