RetrogeneDB ID: retro_sara_341

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_172314:6770..7593(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A46
• Ensembl ID: ENSSARG00000001814
• Aliases: None
• Description: solute carrier family 25, member 46 [Source:HGNC Symbol;Acc:25198]

Sequence

>retro_sara_341
AATGTACTGGCCCATCCTTGCATTGTTCTGCGCCGACAGTGTCAGGTTAATTACCATGCTCGGTATTATCACCTCACTCC
ATTTACAGTCATAAATATTATGTATAGCTTCAACAAAACTCAGGGAACCACGAGCCCTGTGGAAAGGAATGGGAAGTACG
TTTATTGTCCAGGGGGTGACACTTGGAGCAGAGGGACTAATCAGTGAATTCACACCTTTGCCAAGGGAGGTTTCACATAA
ATGGAATCTTACACAAATCGCAGAACACCTTTTACTAAAATCTCTAACTTACATGGTGGCAATGCCCTTTTATTCAGCAA
GTCTAATTGAAACCGTACAGAGTGAGATCATTCGAGATAACACTGGAATTTTGGAGTGTGTCAGAGAAGGACTTGGAAGA
GTGTTAGGCTTGGGAGTGCCTCATAGCAAACGACTACTTCCTCTTCTTTCCTTGATCTTCCCTACTGTGCTGCACGGGGT
TCTTCATTACATCATCAGTTCACTCATTCAGAAGTTGGTCCTACTAGTTCTAAAGAGAAAGACTTACAGTAGCCACTTAG
CTGAGAGCACTAGTCCTGTACAGTGTATGTTGGATGCTTATTTTCCAGAACTTATTGCTAACTTTGCTGCCAGTCTGTGC
TCTGACATTATACTTTACCCATTGGAAACAGTCTTGCACAGCCTTCACATTCAAGGAACACGCACAATAATTGACAATAC
AGACCTTGGCTATGAAGTGCTTCCAATTAACACACAGTATGAGGGCATGAGGGACTGCATCAACACCATCAGGCAGGAGG
AAGGAGTGTTTGGTTTTTATAAA

Alignment

ORF - retro_sara_341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.73 %
• Parental protein coverage: 68.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVLAHPCIVLRRQCQVNYHARYYHLTPFTVINIMYSFNKTQG-PRALWKGMGSTFIVQGVTLGAEGLISE
          NVLAHPCIVLRRQCQVNYHARYYHLTPFTVINIMYSFNKTQG.PRALWKGMGSTFIVQGVTLGAEGLISE
Retrocopy NVLAHPCIVLRRQCQVNYHARYYHLTPFTVINIMYSFNKTQG>PRALWKGMGSTFIVQGVTLGAEGLISE

Parental  FTPLPREVSHKWNLTQIAEHLLLKSLTYMVAMPFYSASLIETVQSEIIRDNTGILECVREGLGRVLGLGV
          FTPLPREVSHKWNLTQIAEHLLLKSLTYMVAMPFYSASLIETVQSEIIRDNTGILECVREGLGRVLGLGV
Retrocopy FTPLPREVSHKWNLTQIAEHLLLKSLTYMVAMPFYSASLIETVQSEIIRDNTGILECVREGLGRVLGLGV

Parental  PHSKRLLPLLSLIFPTVLHGVLHYIISSLIQKLVLLVLKRKTYSSHLAESTSPVQCMLDAYFPELIANYA
          PHSKRLLPLLSLIFPTVLHGVLHYIISSLIQKLVLLVLKRKTYSSHLAESTSPVQCMLDAYFPELIAN.A
Retrocopy PHSKRLLPLLSLIFPTVLHGVLHYIISSLIQKLVLLVLKRKTYSSHLAESTSPVQCMLDAYFPELIANFA

Parental  PSQYT-TIHFQLDKVHSRRILKGTCTSWHNTSSGY-ALPPNPQSKGRTARSIAIGQEEGVSLFYK
          .S.....I...L..V.......GT.T...NT..GY..LP.N.Q..G.......I.QEEGV..FYK
Retrocopy ASLCSDIILYPLETVLHSLHIQGTRTIIDNTDLGYEVLPINTQYEGMRDCINTIRQEEGVFGFYK

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_341 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012366	1 retrocopy	retro_ocun_694,
Sorex araneus	ENSSARG00000001814	1 retrocopy	retro_sara_341 ,