RetrogeneDB ID: retro_oind_81

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 3:5537564..5538338(-)
• Located in intron of: BGIOSGA011281

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA001352
• Aliases: None
• Description: None

Sequence

>retro_oind_81
TTGCACTCCTCGTTAAGTGATTCCTCCAATGTATCACAAGAGAAAATAGTGATAACAAACAGATATGGAGAGAAAATCGT
TGGTCTTTTGCATGAAGCTGGATCTAACGATATTGTAGTTTTGTGCCATGGATTTAGGTCATCAAAGGAAAGTAGAACCA
TACTATGTCTCAGTGATGCACTAACTTCAGAAAATATTAGCGTATTTCGTTTTGATTTCACTGGCAATGGAGAAAGTGAA
GGCACATTCCAGTATGGCAACTATTACAAAGAGGTGGATGATTTGCGTGATGTAATTCTACATTTCAAGAAACACAAGCG
TGACACCCGCGGTATTGCTGGCCACAGTAAAGGAGGAAATGTGGTCATCCTGTATTCATCCATTCATCGAGATGTAGCTA
GTATTATTAACATGTCTGGAAGATTTGATCTAAGACGTGGAATTGCTGATCGTCTTGGAAGTGATTATATGGAAAAGATA
GACCGGTATGGGTTCATTGATGTGGGAGTGAAAACAGGACGTTCCATCTACCGTGTAACCAAAGAAAGTCTGATGGATCG
CCTTAAGATAGATATGAAGAGTTCATGCATGTCTATTGATCCTAAATGCAGGGTTCTGACAATTCATGGTTCTGATGATG
ATATTGTGCCATCAGAGGATGCCCTAGAATTTGACAAATATATAAGCAATCATGAATTGAGTATTATTGAAGGAGCTGAT
CATAGATATTCATTGCATCACCTTGAGTTGGCTACCATTGTACTGAAATTTATT

Alignment

ORF - retro_oind_81 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.23 %
• Parental protein coverage: 94.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSSSQDSSVPSAQEERVVVTNKHGEKLIGLLQHMGSNKIVVICHGFTASKNDSIIVDLANALTKKGVGI
          L.SS..DSS......E..V.TN..GEK..GLL...GSN.IVV.CHGF..SK....I..L..ALT......
Retrocopy LHSSLSDSS--NVSQEKIVITNRYGEKIVGLLHEAGSNDIVVLCHGFRSSKESRTILCLSDALTSENISV

Parental  FRFDFSGNGESEGEFQYGNYRKEADDLHSVISHLNQEKYDVKAIVGHSKGGDVVVLYASIYDDVRTVVNL
          FRFDF.GNGESEG.FQYGNY.KE.DDL..VI.H....K.D...I.GHSKGG.VV.LY.SI..DV....N.
Retrocopy FRFDFTGNGESEGTFQYGNYYKEVDDLRDVILHFKKHKRDTRGIAGHSKGGNVVILYSSIHRDVASIINM

Parental  SGRFHLEKGIEERLGKEFMNIIDKEGYIDVKTNSGKVLYKVTKESLMERLTTDMHKACLSISKECRFFTV
          SGRF.L..GI..RLG...M..ID..G.IDV....G...Y.VTKESLM.RL..DM...C.SI...CR..T.
Retrocopy SGRFDLRRGIADRLGSDYMEKIDRYGFIDVGVKTGRSIYRVTKESLMDRLKIDMKSSCMSIDPKCRVLTI

Parental  HGSADEIIPVEDAYEFAKHIPNHKLHVIEGANHCYTAHRKELSDAVVDFI
          HGS.D.I.P.EDA.EF.K.I.NH.L..IEGA.H.Y..H..EL...V..FI
Retrocopy HGSDDDIVPSEDALEFDKYISNHELSIIEGADHRYSLHHLELATIVLKFI

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_81 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G47590	1 retrocopy	retro_atha_5,
Oryza sativa indica	BGIOSGA001352	1 retrocopy	retro_oind_81 ,
Brassica oleracea	Bo3g134660	1 retrocopy	retro_bole_24,
Brassica rapa	Bra019508	1 retrocopy	retro_brap_47,
Hordeum vulgare	MLOC_20645	1 retrocopy	retro_hvul_20,
Populus trichocarpa	POPTR_0018s06860	1 retrocopy	retro_ptri_17,