RetrogeneDB ID: retro_sara_560

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_233695:7901..9548(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000009972
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSSARG00000010799
• Aliases: None
• Description: dermatan sulfate epimerase [Source:HGNC Symbol;Acc:21144]

Sequence

>retro_sara_560
CATCCAAGTTTGTATTTTGATGCTGGAGAGATCCAGGCCCTGCGACAAAAGTCTCGCACCAGCCATTTGCATCTCTTTAG
AGCCCTCCGAAGTGCAGTGACAGCTATGCTATCCAATCCCACCTACTACCTACCTCCACCCAAGCATGCTGATTTTGCTG
CCAAGTGGAATGAAATTTATGGTAACAATCTGCCTCCGTTAGCACTGTACTGTTTGCTGTGCCCGGAAGACAAAGTCGCC
TTTGACTTTGTCTTGGAATATATGGACAGGATGGTCAGCTACAAGGACTGGCTGGTTGAGAACGCACCCGGAGATGAAGT
ACCCATTGGCCACTCCTTAACAGGTTTTGCCACGGCTTTTGATTTTTTATGTAACTTGTTAGATGACCACCGAAGACAAA
GATACCTGGACAAAATCGTGGTTATCACTGAGGAGATGTATGAGTATTCCAAGGTCCGCTCTTGGGGTAAACAGCTTCTC
CATAACCACCAAGCCACTAATATGATCGCGTTACTCACTGGGGCCTTGGTGATTGGGATAGATAAAGGACCCGAAGTGAA
TGTATGGAAACAGGTCGTAGTAGATGTGATGGAAAAGACAATGTTTCTTTTGAATCATATTGTGGATGGTTCTTTGGATG
AAGGTGTGGCTTACGGAAGCTACACAGCTAAATCAGTCACACAGTATGTTTTTCTAGCCCAGCGCCATTTTAATATCAAC
AACTTGGACAATAACTGGTTAAGAATGCACTTTTGGTTCTATTACGCCACCCTTTTGCCTGGCTTCCAAAGAACTGTGGG
CATCGCAGATTCCAACTATAATTGGTTTTATGGCCCAGAGAGTCAGTTGGTTTTCTTGGATAGATTCATCTTAAGGAACG
GAGCTGGAAACTGGTTAGCCCAGCAAATCAGAAAGCACCGGCCGAAAGATGGACCAATGGTCCCTTCGACCGCTCAGAGG
TGGAGCACTCTTCACACGGAGTACATCTGGTATGATCCCCAACTCACCCCACAGCCCCCTGCTGAATATGGCACTGCAAA
AATGCACGTGTTCCCTAACTGGGGCGTGGTCACCTATGGCGCTGGCCTGCCGAACACACAGACAAATACCTTCATGTCTT
TTAAGTCCGGGAAGCTCGGAGGGCGAGCTGTGTACGACATAGTTCACTTCCAGCCATACTCCTGGATCGATGGGTGGAGA
AGCTTCAACCCGGGCCACGAGCATCCAGATCAGAATTCGTTTACATTTGCCCCCAACGGGCAAGTGTTTGTTTCCGAAGC
TCTCTATGGACCCAAGCTCAGCCACCTGAACAACGTGCTGGTCTTCGCCCCGTCTCCCACAAGCCAGTGTAACAAACCCT
GGGAGGGCCAGCTGGGAGAGTGTGCACAGTGGCTCAAGTGGACGGGCGAGGAGGTCGGTGATGCAGCTGGAGACATCATC
ACTGCCTCCGAACAGGGGGAGATGGTGTTTGTGAGCGGGGAGGCCGTGTCTGCGTACTCTTCAGCCATGAAGCTGAGAAG
TGTGTATCGGGCACTGCTTCTCTTAAACTCTCAAACTTTGCTCGTGGTCGATCATGTGGAGAAGCAACGTGATTCCCCGC
TGAAATCCGTCAGTGCCTTCTTTCATAATCTGGATATTGATTTTAAG

Alignment

ORF - retro_sara_560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.79 %
• Parental protein coverage: 57.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HPMLFFSRAEVSELQLRATSSHKHIAARLTEAVHAMLTSPLEYLPPWDPKDYSARWNEIYGNNLGALAMY
          HP.L.F...E...L......SH.H....L..AV.AML..P..YLPP....D..A.WNEIYGNNL..LA.Y
Retrocopy HPSLYFDAGEIQALRQKSRTSHLHLFRALRSAVTAMLSNPTYYLPPPKHADFAAKWNEIYGNNLPPLALY

Parental  CVLYPENIEARDMAKDYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIA
          C.L.PE...A.D....YM.RM.....WLV..AP.DEVP..HSL.GFATA.DFL.N.L........L..I.
Retrocopy CLLCPEDKVAFDFVLEYMDRMVSYKDWLVENAPGDEVPIGHSLTGFATAFDFLCNLLDDHRRQRYLDKIV

Parental  NASGYMYETSYRRGWGFQYLHNHQPTNCMALLTGSLIL-MNQGYLQEAYLWTKQVLTIMEKSLVLLREVT
          .....MYE.S..R.WG.Q.LHNHQ.TN..ALLTG.L......G...E...W...V...MEK...LL....
Retrocopy VITEEMYEYSKVRSWGKQLLHNHQATNMIALLTGALVIGIDKG--PEVNVWKQVVVDVMEKTMFLLNHIV

Parental  DGSLYEGVAYGSYTTRSLFQYMFLVQRHFDINHFGHPWLKQHFSFMYRTILPGFQRTVAIADSNYNWFYG
          DGSL.EGVAYGSYT..S..QY.FL.QRHF.IN.....WL..HF.F.Y.T.LPGFQRTV.IADSNYNWFYG
Retrocopy DGSLDEGVAYGSYTAKSVTQYVFLAQRHFNINNLDNNWLRMHFWFYYATLLPGFQRTVGIADSNYNWFYG

Parental  PESQLVFLDKFVMRNGSGNWLADQIRRSRVLEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTL
          PESQLVFLD.F..RNG.GNWLA.QIR..R...GP..PS..QRW.TLHTE..WYD..L...PP...GT...
Retrocopy PESQLVFLDRFILRNGAGNWLAQQIRKHRPKDGPMVPSTAQRWSTLHTEYIWYDPQLTPQPPAEYGTAKM

Parental  HYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFA
          H.F..WGVVTYG..LP......F.SFKSGKLGGRA.YDIVH...Y..WI.GWR.FN.GHEHPDQNSFTFA
Retrocopy HVFPNWGVVTYGAGLPNTQTNTFMSFKSGKLGGRAVYDIVHFQPY-SWIDGWRSFNPGHEHPDQNSFTFA

Parental  PNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAVEK
          PNG..F..EALYGPK....NNVL.F.P.....C..PWEGQ..E.....W.K..........G....A.E.
Retrocopy PNGQVFVSEALYGPKLSHLNNVLVFAPSPTSQCNKPWEGQLGE--CAQWLKWTGEEVGDAAGDIITASEQ

Parental  NGVVFIRGEGVGAYNPQLKLKHVQRNLILLHPQLLLLVDQIHLGEDTPLESVASFFHNVDVPFE
          ...VF..GE.V.AY....KL..V.R.L.LL..Q.LL.VD......D.PL.SV..FFHN.D..F.
Retrocopy GEMVFVSGEAVSAYSSAMKLRSVYRALLLLNSQTLLVVDHVEKQRDSPLKSVSAFFHNLDIDFK

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_560 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560 ,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,