RetrogeneDB ID: retro_sara_395

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_191288:8943..9463(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIM2
• Ensembl ID: ENSSARG00000008832
• Aliases: None
• Description: pim-2 oncogene [Source:HGNC Symbol;Acc:8987]

Sequence

>retro_sara_395
GTGGCCATCAAGCACGTGGAGAAGGACCGGATTTCCAACTTGGGTGAGCTGCCCAACCGCACCCGCGTGCCCATGGAGGT
GTTCCTGCTGAGGAAGGTGGGCTTGGGCTTCCCCGGCGTCACCCGCCTCCTTGACTGGTTCGAGCGGCCCAAAGAGCTTC
GTGCTGGTGCTGGAGCGGCCCGAGCTGGTGCAGGACCTGTTCAACTTCACACGGAGCGCGGCGCGTTGCAAGAGGAGCTG
ACCTGCAGCTTCTTGTGGCAGGTGCTGGAGGCTGTGCTGCACTGCCACAGAGGCGGGGTGCTGCGCTGCGGCATCGAGGA
TGAGAACATCCTCATCGACCTGGCGCTGTGGCAAGCTTAAACTCATCGACTTCGGCTTGGGGGCGCTGCTCAAGGACACG
GTCTACACGGACTTCGATGGGACCCGAGTGTATAGTCCTCCTGAGTGGATCCGCTACCATCGCTACACTGGCAGGATGGC
TGCGGTCTGGTCCCTGGGGATCCTGATGTGCGATATAGTC

Alignment

ORF - retro_sara_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.74 %
• Parental protein coverage: 68.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VAIKVIPRNRVLDWSPLPDSGTCPLEVALLWKVGAGGGHPGVIRLLDWFETAE-GFMLVLERPLPAQDLF
          VAIK.....R......LP.....P.EV.LL.KVG.G...PGV.RLLDWFE.....F.LVLERP...QDLF
Retrocopy VAIKHVEKDRISNLGELPNRTRVPMEVFLLRKVGLG--FPGVTRLLDWFERPK>SFVLVLERPELVQDLF

Parental  DYI-TEQGPLGENRSRSLFAQVVAAVRHCHARGVVHRDIKDENILMDL-RRGCAKLIDFGSGALLHDEPY
          ....TE.G.L.E....S...QV..AV.HCH..GV....I.DENIL.DL.R.G..KLIDFG.GALL.D..Y
Retrocopy NFT<TERGALQEELTCSFLWQVLEAVLHCHRGGVLRCGIEDENILIDL>RCGKLKLIDFGLGALLKDTVY

Parental  TDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMV
          TDFDGTRVYSPPEWI..H.Y....A.VWSLGIL..D.V
Retrocopy TDFDGTRVYSPPEWIRYHRYTGRMAAVWSLGILMCDIV

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_395 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223, retro_sara_395 ,