RetrogeneDB ID: retro_sara_569

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_234856:87088..87956(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2E2
• Ensembl ID: ENSSARG00000007758
• Aliases: None
• Description: general transcription factor IIE, polypeptide 2, beta 34kDa [Source:HGNC Symbol;Acc:4651]

Sequence

>retro_sara_569
ATGGATCCAAGCCTGCTGAGAGAACGGAAGCTATTCAAAAAACGAGCTCTTTCCACTCCTCATATTGAAGACAGATCAGG
AACTGCTGGCTCATCGTCATCGTCATCACCTGGGAAGAAGAAAGCAAAACTAGAACATGGAGGTTCATCAGTCTCTAAAC
AAAATTCTGATTATAGCAATGGATCATTGAACTTGAAAGGTCTGTCGGGAGGCTCTGGATATCAGGTTGGTGTTCTTATG
AAGGTTGTGAATTTCATGAAAACACGGCATCAGAGAGGAGACACACATCCTCTCCCTTTGGAAGAAATTCTGGATGAAAC
AGAGCACTTAGATATCGAACTCAAGCAGAAGCTGTGTCTTATGAGTGAGGCTTTAGTCAAGAATCCCAAAATCGAGGTCA
TCGATGGAAGTAGCCTTCAAGCCAAGCACAGGCTGAAGATGAGACGGCCCTGCTCCGGCTCTTACAGCAGCATGAGCAGC
GAGGCTTGGGAGGATTCTTCTGGAAGGCATAGAGAAGGACTTCCCAGGGACCCAGAAAGCTCCCAAGGCCTTAGGGGACC
AGATACTATTTGTCAATCGACGGATAAGTAGAAAATTGTTTTCTTCAACGATAAGAGCTGTGGATTTTCTGTCGATGAGG
AGTTTCAGAAACTGTGGAGGAGTGTCCCTGTGGGCTCCATGGATGAGGAGAACATTGCAGAGTCCTGAGGTATCAGGGAA
TTTCCTCCATGCAGGGTACCGGACCCAAAAGAGTGGCCCTATCCAGAGAAGGGCAAAGCCTGCTTCGCAGAAGAAGAGGC
GCTGTAAGATGCAGAATGAGCACTTGGTGGGAGTGCTAAAGGAGTACTCAGGCACGGCGCCCGGGAAG

Alignment

ORF - retro_sara_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDPSLLRERELFKKRALSTPVIEKRSVTASSSSSSSSKKKKAKLDHGGSSGSKQNSDHSNGSFNFKALSG
          MDPSLLRER.LFKKRALSTP.IE.RS.TA.SSSSSS..KKKAKL.HGGSS.SKQNSD.SNGS.N.K.LSG
Retrocopy MDPSLLRERKLFKKRALSTPHIEDRSGTAGSSSSSSPGKKKAKLEHGGSSVSKQNSDYSNGSLNLKGLSG

Parental  SSGYKFGVLAKIVNYMKTRHQRGDTHPLTLEEILDETQHLDIGLKQKQWLMSEALVNNPKIEVVNGKYAF
          .SGY..GVL.K.VN.MKTRHQRGDTHPL.LEEILDET.HLDI.LKQK..LMSEALV.NPKIEV..G....
Retrocopy GSGYQVGVLMKVVNFMKTRHQRGDTHPLPLEEILDETEHLDIELKQKLCLMSEALVKNPKIEVIDGS-SL

Parental  KPKYNLK-DKKALLRLLDQHDQRGLGG-ILLEDIEEGLPNSQKAVKALGDQILFVNR-PDKKKILFFNDK
          ..K..LK.D..ALLRLL.QH.QRGLGG.ILLE.IE...P..QKA.KALGDQILFVNR..DK.KI.FFNDK
Retrocopy QAKHRLK<DETALLRLLQQHEQRGLGG<ILLEGIEKDFPGTQKAPKALGDQILFVNR<TDK*KIVFFNDK

Parental  SCQFSVDEEFQKLWRSVTVDSMDEEKIEE-YLKRQGISSMQDSGPKKVA-PIQRRKKPASQKKRRFKTHN
          SC.FSVDEEFQKLWRSV.V.SMDEE.I.E..L..QGISSMQ..GPK.VA.PIQRR.KPASQKKRR.K..N
Retrocopy SCGFSVDEEFQKLWRSVPVGSMDEENIAE<VLRYQGISSMQGTGPKRVA<PIQRRAKPASQKKRRCKMQN

Parental  EHLAGVLKDYSDMAPGK
          EHL.GVLK.YS..APGK
Retrocopy EHLVGVLKEYSGTAPGK

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_569 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005031	1 retrocopy	retro_dnov_2321,
Macropus eugenii	ENSMEUG00000010541	1 retrocopy	retro_meug_546,
Myotis lucifugus	ENSMLUG00000007814	1 retrocopy	retro_mluc_2029,
Sorex araneus	ENSSARG00000007758	2 retrocopies	retro_sara_376, retro_sara_569 ,
Sus scrofa	ENSSSCG00000015845	1 retrocopy	retro_sscr_878,
Tarsius syrichta	ENSTSYG00000013143	1 retrocopy	retro_tsyr_2074,
Tursiops truncatus	ENSTTRG00000012464	1 retrocopy	retro_ttru_859,