RetrogeneDB ID: retro_sara_97

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_2823:154045..154414(+)
• Located in intron of: ENSSARG00000010673

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2B
• Ensembl ID: ENSSARG00000004969
• Aliases: None
• Description: RAB2B, member RAS oncogene family [Source:HGNC Symbol;Acc:20246]

Sequence

>retro_sara_97
AAATCTGTGATATGGGGAGCTGCTGGAGTGCTGCTTGTATATAACGTTAAGAGCATGAAACCTTCAGCCTTCTGTCATAG
CTAGAGAATTTGTGGCAGCACTCAAGTTCCAACATGGTCATTATGGTGATAAGGAATAAGTGTGACTTAGAAACTTGCAA
AGACGTGAAGAAAGGAGAGGTCTTTGTTCAGGAGCATGGGCTTATATTCACTGAAAAGTCAGCTAAAACAGCTTAATGTT
GAAGAGGCCTTCATTAACACAGCCAAAGAAACATATTGGAAGATCCATCAGGGTTTACTTGATGTCAGCAATGAGGCAAA
TGGCTTCAAGATTGATAGCCAACAATGTCATTCAATATCAGTGGAACCT

Alignment

ORF - retro_sara_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.69 %
• Parental protein coverage: 58.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSYYRGAAGALLVYDIT-RRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKKEEGEAFAREH
          .S...GAAG.LLVY......ETF..L.S.LE...QHSSSNMVIM.I.NK.DLE...DVKK..GE.F..EH
Retrocopy KSVIWGAAGVLLVYNVK<EHETFS-LLS*LENLWQHSSSNMVIMVIRNKCDLETCKDVKK--GEVFVQEH

Parental  -GLIFMETSAKTACNVEEAFINTAKEIYRKIQQGLFDVSNEANGIKIGPQQSISTPVGP
          .GL.......K...NVEEAFINTAKE.Y.KI.QGL.DVSNEANG.KI..QQ..S..V.P
Retrocopy >GLYSLKSQLKQL-NVEEAFINTAKETYWKIHQGLLDVSNEANGFKIDSQQCHSISVEP

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_97 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97 ,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688, retro_sara_744,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468,