RetrogeneDB ID: retro_olat_37

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 24:17287534..17287844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN2 (1 of 2)
• Ensembl ID: ENSORLG00000008251
• Aliases: None
• Description: stathmin-like 2 [Source:HGNC Symbol;Acc:10577]

Sequence

>retro_olat_37
CCCAAAAAGAAGGACATCTCCCTGGAGGAGATTCAGAGAAAGCTGGATGCCGCAGAGGGAAGACGCAAGAACCATGAAGC
CGAGGTTCTGAAGCACCTAGCTGAGAAGCGAGAGCACGAAAAGGAGGTGCCACAGAAAGCAATGGAGAAGAACAACAACT
TCAGCAAGATGGCAGAGGAGAAGCTCAACCAAAAGATGGAGGCCAACAAGAAGAACCGCAGCTGCCATCATGGCAGCCAT
TAACGAGAAGTTCATGGAGAAGGACAAGAAGTTGGAAGAGGTGCGAAAGAACAAGGAGACCAAAGATCAG

Alignment

ORF - retro_olat_37 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.58 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPKRDISLEDIEKKLEAAEERRKYQEAQVLRALAEKREHERDVLLKAMEENSNFSKMAEEKLHMKMEQIK
          P.K.DISLE.I..KL.AAE.RRK..EA.VL..LAEKREHE..V..KAME.N.NFSKMAEEKL..KME..K
Retrocopy PKKKDISLEEIQRKLDAAEGRRKNHEAEVLKHLAEKREHEKEVPQKAMEKNNNFSKMAEEKLNQKMEANK

Parental  ENREAH-MAAMMERLLEKEKRAVVVRRNKELREE
          .NR..H.MAA..E...EK.K....VR.NKE....
Retrocopy KNRSCH>MAAINEKFMEKDKKLEEVRKNKETKDQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_37 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_37 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003373	3 retrocopies	retro_dnov_2381, retro_dnov_545, retro_dnov_831,
Dipodomys ordii	ENSDORG00000005974	1 retrocopy	retro_dord_302,
Mustela putorius furo	ENSMPUG00000001863	1 retrocopy	retro_mputfur_68,
Otolemur garnettii	ENSOGAG00000027869	2 retrocopies	retro_ogar_2664, retro_ogar_330,
Oryzias latipes	ENSORLG00000008251	1 retrocopy	retro_olat_37 ,
Sorex araneus	ENSSARG00000010989	1 retrocopy	retro_sara_756,
Ictidomys tridecemlineatus	ENSSTOG00000025094	2 retrocopies	retro_itri_1012, retro_itri_1423,
Tarsius syrichta	ENSTSYG00000014759	1 retrocopy	retro_tsyr_26,