RetrogeneDB ID: retro_sara_689

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_259051:37861..38436(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSSARG00000006615
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_sara_689
GGGACCAACTCCAGAACAACCACTGGGTCCTACATCGCCAATCGAGTGACTGACAAGCTGACATCTATTCATGATGGACT
TTTCTGCTGCCACTCTGGCTCAGCAGCTGGTACCCATGCAGTCACTGATGCGATCACTTACCAGCCTGGTTTCCACAGCA
TTGAACTGTATGAGTCTGCTTTAGTACACACAGCAGCCAGCCTCTTTAAGGAGATGTGTTACCGATACCGAGAAGATCTG
ATGGCAGGAATCATCATTGCAGGCCGGGATCACTAAGAAGGAGGTCAGGTATATACTCAGTGCCCATGGGGAGTATGATG
GTACAGCAGCCCTTTGCCATTGGGGGCTCTGGGAGAGCCTATATCTATGGCTATGTTGATGCTACCGACCGGGAAGGCAT
GACCAAGGAAGAATGTTGCAGTTCATTGCTAATACTCTCGCTTTGGCCATGGAGGGGGACGGCTCCAGTGGAGGAGTCCT
CTGCCTGGAGCCATTGCAGAATCAGAGGGGTAGAGTGGCAGTTACTTTTGGGAAATCAGATCCCCAAATTTGCCAGTGCC
ACTTTGCCACCTCCC

Alignment

ORF - retro_sara_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.26 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GADSRTTTGSYA--RVTDKLP--HDRI--CRSGSAADTQ-VADAVTYQLG-HSIELNEPPLVHTAASLFK
          G..SRTTTGSY...RVTDKL...HD....C.SGSAA.T..V.DA.TYQ.G.HSIEL.E..LVHTAASLFK
Retrocopy GTNSRTTTGSYIANRVTDKLTSIHDGLFCCHSGSAAGTHAVTDAITYQPGFHSIELYESALVHTAASLFK

Parental  EMCYRYREDLMAGIIIAGWDHQEGGQVYS-VPMG-GMMVKQPFAIGGSGSSYIYGYVDATYREGMTKEEC
          EMCYRYREDLMAGIIIAG.DH.EGGQVY...P.G..MMV.QPFAIGGSG..YIYGYVDAT.REGMTKEEC
Retrocopy EMCYRYREDLMAGIIIAGRDH*EGGQVYTQCPWG<SMMVQQPFAIGGSGRAYIYGYVDATDREGMTKEEC

Parental  -LQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIP-KFASATLPPP
          .LQF.AN.LALAME.DGSSGGV..L...........V..G...P.KFASATLPPP
Retrocopy <LQFIANTLALAMEGDGSSGGVLCLEPLQNQRGRVAVTFGKSDP>KFASATLPPP

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_689 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Felis catus	ENSFCAG00000008036	2 retrocopies	retro_fcat_1813, retro_fcat_1995,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689 ,
Ictidomys tridecemlineatus	ENSSTOG00000014871	1 retrocopy	retro_itri_514,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,