RetrogeneDB ID: retro_sara_143

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_4364:193901..194500(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000002747
• Aliases: None
• Description: None

Sequence

>retro_sara_143
CCTCCAAATCTCACTGCAGCCATTGCTGCAACTGCAATGGCAAAGTGAAGAGGCAGAATCAACAACAATCCTGCACCAAC
AGATTCCAATGCAAGAGCAGGAAAAGTCTGGCAACAAGGAAGATGGAAGCCCCATTGGGCCACCCAGCCTTCTGGGCGCA
CCCCACATGGCCAGTGGAAAGCCTGGCAACTCCAAGTCAGTTCTACACGGAGTTCGTCCAGAATCAAGACCAGTAATTCC
ACAACTGCTGAGTGTGGACACCACATCCTCCCTCGGACAGAGACCCAGTTTGTGGGGGACTTGGGTTCCATGACTGGTCC
ATATTGTTATGGTTGATGGGCAGGTTAACGCTCAACCTCCTTTTCTTAGACCAGGCCATGGGAGTTGCTCCTTGGGTGAC
TCTCACAAAGAACAGAGAAACCCCCAAAGGTTCAAAAGCTGGTTTCTTATAAAAAATACCTGCCCACACAAGGATGGAAC
CCAAGTTACAGAAAACAAATCTGGCCTCCCTGTCTGCCGACAGTTTGCACACATAGGGCCGTAGTAGATACAAGATTTGA
TGTGCCTTCTACCACATAGGCATCGATGGAGCATCTCTT

Alignment

ORF - retro_sara_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.65 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PPNPTAAIAATTMPK-RKKQNQQQPP-HQQPPMPEREEPGDEEDGSLIGPPSLLGPPPMANGKPGDPKSA
          PPN.TAAIAAT.M.K..K.QNQQQ...HQQ.PM.E.E..G..EDGS.IGPPSLLG.P.MA.GKPG..KS.
Retrocopy PPNLTAAIAATAMAK<VKRQNQQQSC<HQQIPMQEQEKSGNKEDGSPIGPPSLLGAPHMASGKPGNSKSV

Parental  LHRGPPESRGPIIPPLLSL-PPPP-RGRGPIRGA-LGPRSTPYGRGWWG-VNAEPPFPGPGHGGPSRGGF
          LH...PESR.P.IP.LLS...P.P...R.P..G..LG....PY..G.W..VNA.PPF..PGHG..S.G..
Retrocopy LHGVRPESR-PVIPQLLSV>TPHPPSDRDPVCGG>LGSMTGPYCYG*WA>VNAQPPFLRPGHGSCSLGDS

Parental  HKEQRNPRRLKSWSLIKNTCPPKDGPQVMEDKSGRPVCRHFA-TKGHCRYEDLCAFYHPGVNGPPL
          HKEQRNP.R.KSW.LIKNTCP.KDG.QV.E.KSG.PVCR.FA.T.G..RY...CAFYH.G..G..L
Retrocopy HKEQRNPQRFKSWFLIKNTCPHKDGTQVTENKSGLPVCRQFA>T*GRSRYKI*CAFYHIGIDGASL

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_143 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022770	1 retrocopy	retro_cpor_775,
Felis catus	ENSFCAG00000025918	2 retrocopies	retro_fcat_1094, retro_fcat_1698,
Gorilla gorilla	ENSGGOG00000014604	1 retrocopy	retro_ggor_1915,
Myotis lucifugus	ENSMLUG00000008758	1 retrocopy	retro_mluc_1567,
Macaca mulatta	ENSMMUG00000013893	1 retrocopy	retro_mmul_1431,
Nomascus leucogenys	ENSNLEG00000005104	1 retrocopy	retro_nleu_1548,
Otolemur garnettii	ENSOGAG00000004430	2 retrocopies	retro_ogar_1030, retro_ogar_1324,
Pongo abelii	ENSPPYG00000016409	1 retrocopy	retro_pabe_2279,
Pan troglodytes	ENSPTRG00000017929	1 retrocopy	retro_ptro_1861,
Sorex araneus	ENSSARG00000002747	2 retrocopies	retro_sara_143 , retro_sara_9,
Ictidomys tridecemlineatus	ENSSTOG00000011829	1 retrocopy	retro_itri_126,
Tarsius syrichta	ENSTSYG00000000166	2 retrocopies	retro_tsyr_308, retro_tsyr_841,