RetrogeneDB ID: retro_sara_518

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_229886:176663..177512(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000011446
• Aliases: None
• Description: None

Sequence

>retro_sara_518
TGGTTTGGCCAGGATAAACAGTATAATATACTGGTCATAGATCTTCTCGGACCCAGCCTGGAAGATCTCTTCAATCTCTG
CTCAAGAAAGTTCTCAATGAAAACCATACTCATGTTAGCTGACCAGATGATATGTAGGCTTGAATATCTGCATAGCCGAA
ATTTTATACACAGAGATATTAAACCAGAAAACTTCCTGATGGGTGCTAGCTGCCAGTGTTTCAAATGTTTAGGCACTTTT
GAAGGACAAAGGAAAAGGATCATGTTAAATTATCAGAACCAGCCTTATGCAAAATTAAACCAGGTATTTCTGGTAGATTT
TGGCTTGGCAAAGAAGTACAGAGAAAATAAAACAAAGGAACATATACCATACAGAGACGATAAACATCTAACTGGCACCG
CCCGATATGCTAGCATTAATGCTCACCTTGGTATTGAGCAAAGTCGCCGAGATGATATGGAGGCCTTAGGATATGTTTTG
ATGTACTTTAATAGAAGTGGCCTGCCATGGCAAGGATTAACAGGTGCCACAAGGAAACAAAAGTATGAGAAGATTCGTGA
AAAGAAGTTAGCCACTTCCATTGATGTTTTATGTAAAGGCTTCCCTGCAGAATTTGCCATGTATTTAAACTATTGCCGTG
GGCTGCGTTTTGATGAAGTCCCAGATTACGGGTATCTGAGGCAGCTATTTCATGTTCTTTTCAAGACCTTGAACTATCAA
CATGATTACATATTTGACTGGACCATTTTAAGTCAGGTGCCACCGAAGCCATCCCCTTCAATATTGCAAGTGCAACCGGA
GCAACCTCCTACTGAGAATCCTGTTGACAAGACCACTGCTTGTAAGAAA

Alignment

ORF - retro_sara_518 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIG
          W.GQ.K.YN.LV.DLLGPSLEDLFN.CSR.F.MKT.LMLADQMI.R.EY.H..NFIHRDIKP.NFLMG..
Retrocopy WFGQDKQYNILVIDLLGPSLEDLFNLCSRKFSMKTILMLADQMICRLEYLHSRNFIHRDIKPENFLMGAS

Parental  RHCNKCLESPVGKRKRSMTVSTSQDPSFSGLNQLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYAS
          ..C.KCL....G.RKR.M.....Q......LNQ.FL.DFGLAKKYR.N.T..HIPYR.DK.LTGTARYAS
Retrocopy CQCFKCLGTFEGQRKRIML--NYQNQPYAKLNQVFLVDFGLAKKYRENKTKEHIPYRDDKHLTGTARYAS

Parental  INAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMY
          INAHLGIEQSRRDDME.LGYVLMYFNR..LPWQGL..AT.KQKYEKI.EKK..T...VLCKGFPAEFAMY
Retrocopy INAHLGIEQSRRDDMEALGYVLMYFNRSGLPWQGLTGATRKQKYEKIREKKLATSIDVLCKGFPAEFAMY

Parental  LNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDK
          LNYCRGLRF.E.PDY.YLRQLF..LF.TLN.Q.DY.FDWT.L.Q........S..Q.Q..Q.PT....DK
Retrocopy LNYCRGLRFDEVPDYGYLRQLFHVLFKTLNYQHDYIFDWTILSQ-VPPKPSPSILQVQPEQPPTENPVDK

Parental  TKSNMK
          T....K
Retrocopy TTACKK

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_518 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 17 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Sorex araneus	ENSSARG00000005475	1 retrocopy	retro_sara_33,
Sorex araneus	ENSSARG00000009110	2 retrocopies	retro_sara_287, retro_sara_337,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518 ,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,