RetrogeneDB ID: retro_opun_2

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:261466..262888(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G00380
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G01760
• Aliases: None
• Description: None

Sequence

>retro_opun_2
ATGAGAGCATTTAATTTGTTGGCACAGCTTCTCCGGTCCGTATGCGTCCTCCTCCTGGCCTCGTCGGCGACGGTGGCGGC
GCGGCGCCACGGCCCGGCGGCGCCTATCGCCGGGCAGAGCATGTACCTGGCGCCGAGCTGCCGCGCGCACACGGCGTCGC
TGACGGACTTCGGCGGCGTGGGCGACGGCACGACGTCGAACACGGCGGCGTTCAAGTCGGCTGTGGACCACCTGTCGCAG
TACTCCGGCGAGGGCGGCGGCGGCGCGATGCTGTACGTGCCGGCGGGGAAGTGGTTGACGGGGCCGTTCAACCTGACGAG
CCACTTCACCCTCTTCCTCCACAGCGACGCCGTCATCCTCGGCTCCCAGGACATGGCGGAGTGGCCCATCATCGATCCCC
TCCCCTCCTACGGCCGCGGGCGCGACAAGGCCGGCGGGCGGTACGCCAGCCTGATCGGCGGGTCGAACCTGACGGACGTG
GTGATCACCGGCGCGAACGGGACGATCGACGGGCAGGGGGCGATGTGGTGGTCCAAGTTCCACTCGAACAAGCTCAAGTA
CACGCGTGGGTACCTGATCGAGGTGATGCACTCAGACACGGTGGTGATATCGAACGTGACGCTGGTGAACTCGCCGGCGT
GGAACATCCACCCGGTGTACAGCAGCAACATCGTGGTGCAGGGGGTGACGATCCTGGCGCCGACGCACTCGCCCAACACC
GACGGCATCAACCCGGACTCGTGCTCCCACGTCCGCATCGAGGACTGCTACATCGTCTCCGGCGACGACTGCGTGGCCAT
CAAGTCCGGGTGGGACGAGTACGGCATCGCCTACGGGATGCCCAGCCAGCACATCGTGGTGCGGCGGCTGACGTGCGTGT
CGCCGACGAGCGCCGTGATCGCGCTGGGGAGCGAGATGTCGGGCGGGATCAGCGACGTGCGGGCGGAGGACATAACGGCG
GTGAACTCGGAGTCGGCGGTGCGGATCAAGACGGCGGTGGGTCGGGGGGCGTACGTGCGCGACGTGTTCGTCCGGGGGAT
GTCGCTGGACACGATGAAGTGGGTGTTCTGGATGACGGGGAACTACAAGTCGCACCCCGACGACGGGTACGACCCGAACG
CCATCCCGGTGGTGGAGAACATCAGCTACCAGGACGTGGTGGCGACGGGGGTGTACAAGGAGGCGGCGAGGCTGGAGGGC
ATCCAGGGCGCGCCCTTCCGCGGCATCTGCATCGCCAACGTCACCGCCGCTCTCTCCAAGTCGCGCAAGTACCCGTGGAC
CTGCACCGACATCGAGGGGGTGTCCTCCGCCGTCACGCCGGCGCCGTGCCAGCCGCTGCAGGGGGCGCACGACGGCGCCT
GCCCGTTCCCGACGGACACGCTGCCCATCGACCAGCTCGTCATGCAGCAGTGCGCCATCTAG

Alignment

ORF - retro_opun_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.47 %
• Parental protein coverage: 92.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRKHVAKITEYGGVGDGKRSNTAAFAKAVADLSMRAGDGG--AALVVPEGKWLTGPFNLTSHFTLFLDHG
          CR.H.A..T..GGVGDG..SNTAAF..AV..LS...G.GG..A.L.VP.GKWLTGPFNLTSHFTLFL...
Retrocopy CRAHTASLTDFGGVGDGTTSNTAAFKSAVDHLSQYSGEGGGGAMLYVPAGKWLTGPFNLTSHFTLFLHSD

Parental  AQILASQNLEDWPLIAPLPSYGRGRDEPGPRYSNFIAGSNLTDVIITGKNGTINGQGQVWWDKFHAKELT
          A.IL.SQ....WP.I.PLPSYGRGRD..G.RY...I.GSNLTDV.ITG.NGTI.GQG..WW.KFH...L.
Retrocopy AVILGSQDMAEWPIIDPLPSYGRGRDKAGGRYASLIGGSNLTDVVITGANGTIDGQGAMWWSKFHSNKLK

Parental  YTRGYLLELLHSNNIIISNVTFVDSPSWNLHPTYCTNVTISGITILAPVNSPNTDGIDPDSSSHVKIEDC
          YTRGYL.E..HS....ISNVT.V.SP.WN.HP.Y..N....G.TILAP..SPNTDGI.PDS.SHV.IEDC
Retrocopy YTRGYLIEVMHSDTVVISNVTLVNSPAWNIHPVYSSNIVVQGVTILAPTHSPNTDGINPDSCSHVRIEDC

Parental  YIVSGDDCIAVKSGWDQYGIKFNMPSQHILIRRLTCISPTSAMIALGSEMSGGIRDVRAVDNVAIDTESA
          YIVSGDDC.A.KSGWD.YGI...MPSQHI..RRLTC.SPTSA.IALGSEMSGGI.DVRA.D..A...ESA
Retrocopy YIVSGDDCVAIKSGWDEYGIAYGMPSQHIVVRRLTCVSPTSAVIALGSEMSGGISDVRAEDITAVNSESA

Parental  VRIKSGVGRGGFVKDVFVRGLSLHTMKWVFWMTGNYGQHPDNSSDPNALPEVTGINYSDVFAENV-TMAG
          VRIK..VGRG..V.DVFVRG.SL.TMKWVFWMTGNY..HPD...DPNA.P.V..I.Y.DV.A..V...A.
Retrocopy VRIKTAVGRGAYVRDVFVRGMSLDTMKWVFWMTGNYKSHPDDGYDPNAIPVVENISYQDVVATGVYKEAA

Parental  RLEGIPNDPYTGICISNVTAQLAPDAKKLQWNCTDVKGVTSDVSPKPC-PELGAAGKPCAFPEEELVIGP
          RLEGI...P..GICI.NVTA.L.....K..W.CTD..GV.S.V.P.PC.P..GA....C.FP...L.I..
Retrocopy RLEGIQGAPFRGICIANVTAALS-KSRKYPWTCTDIEGVSSAVTPAPCQPLQGAHDGACPFPTDTLPIDQ

Parental  PELPKCS
          .....C.
Retrocopy LVMQQCA

Legend:

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

Expression

RNA-Seq

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_2 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539266.1_FG011	1 retrocopy	retro_olon_17,
Oryza punctata	OPUNC03G01760	1 retrocopy	retro_opun_2 ,