RetrogeneDB ID: retro_sara_425

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_201736:8614..9440(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSSARG00000004651
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_sara_425
TGGCTTCTAAACAATTTGATGATTCACAACGAATGTTGAAATTTTCAAAGAACTCAGTAAAGTTTCGTTAAACAGCTCAT
TGGCTCATCTAACTTATTTGTGATGCGAGTGGAGATGGATGTAGATACAGCTCTGAAAAAGTGGATGTTTCTTCAACTTG
TGCCTTCTTGGAATGGATCTTGAAAACAGCTTTTGGCTGAAACAGATGTCTGGTTTTCTAAGAGGAAAAGAGATTTTGAA
GGCATGACCTTTCTTGAAACTGAGCAAGGAAAACCGCTTGTGTCATATTCAAGCATTTACGGTTACAGTATATTATCAGT
GATTCAGCCTCTGCATGAATTATGAACAGTATTCTCTAGTACCTTCAGAATGGCGGTATTTTGTGTATAAACAGCAGCGA
CTCCCGGCAGAACAAGTTAGTGAGATGGAGCTTCAATAAATTAACAAAGAAAAACTGGAGGGAAATAGCATGAGGTGTGG
TAGAAAGCTCGCCAGAGATGGTGAATACTGTTGGTGGTGGACAGGTTTTAACTTCAGCTTTGACCTGCTTGTCACTTACA
CCAATCGATACATCATTTTCAAACGCAATACACTGAATCAGTCATGTAGCGGATCTGTCAATTTACAACCTCAAAGGAGC
ATAGTGTTTAGATTATGTTTGGCCTCTTCAGATAGTAGTGGAAAACTAATATGTAGTAGAACAACTCTCTACCGAATACT
TACACTTGAAAAGGATCAGGAACAAGTAGTGATGAACTTGGACAGCAGGCTTCTAATCTTCCCTTTATATATCTGCTGTA
ACTTCTTGTATATATCACCAGAGAAA

Alignment

ORF - retro_sara_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 65.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WLLNNLMTHQ-NVELFKELSI-NVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLTET
          WLLNNLM.H..NVE.FKELS.....KQLIGSSNLFVM.VEMDV.TALKKWMFLQLVPSWNGS.KQLL.ET
Retrocopy WLLNNLMIHN>NVEIFKELSK<SFVKQLIGSSNLFVMRVEMDVDTALKKWMFLQLVPSWNGS*KQLLAET

Parental  DVWFSKRKKDFEGMTFLETEQGKPFVS-VFKHLRLQYIISDLASARII-EQDSLVPSEWLSSVYKQQWLA
          DVWFSKRK.DFEGMTFLETEQGKP.VS..FKHLRLQYIISD.ASA.I..EQ.SLVPSEW...VYKQQ...
Retrocopy DVWFSKRKRDFEGMTFLETEQGKPLVS<IFKHLRLQYIISDSASA*IM<EQYSLVPSEWRYFVYKQQ---

Parental  MLRAEQDSEMGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPC
          .L.AEQ.SEM..Q.INKE.LEGNSMRCGRKLA.DGEYCW.WTGFNF.FDLLVTYTNRYIIFKRNTLNQ.C
Retrocopy RLPAEQVSEMELQ*INKEKLEGNSMRCGRKLARDGEYCWWWTGFNFSFDLLVTYTNRYIIFKRNTLNQSC

Parental  SGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYIS
          SGSV.LQP.RSI.FRL.LAS.DSSGKLICSRTT.Y.ILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYIS
Retrocopy SGSVNLQPQRSIVFRLCLASSDSSGKLICSRTTLYRILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYIS

Parental  PEK
          PEK
Retrocopy PEK

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_425 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425 ,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,