RetrogeneDB ID: retro_oind_50

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 9:4195470..4196271(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA030381
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA003951
• Aliases: None
• Description: None

Sequence

>retro_oind_50
ATGGTGTCCCCAGACTTGATCCGCAACATGGTGGGCATAGTCGGTAACATCATCTCCTTTGGCCTCTTCCTCTCGCCGGT
GCCCACCTTCTACCGGATCATCAAGAATAAGGACGTGCAGGACTTTAAGGCGGACCCGTACCTGGCCACGCTGCTCAACT
GCATGCTCTGGGTTTTCTATGGTCTCCCTATCGTCCACCCCAACAGCATCCTTGTCGTCACCATCAACGGCATTGGCCTT
ATCATCGAGGCTGTCTACCTTACCATCTTCTTCCTCTTCTCCGACAAGAAGAACAAAAAGAAGATGGGAGTGGTGCTCGC
TACGGAGGCTCTCTTCATGGCGGCGGTGGTGCTCGGCGTGCTTTTGGGCGCGCACACCCATCAGAGACGCTCCTTGATCG
TCGGCATCCTCTGCGCCATCTTTGGCACCATCATGTACTCCTCACCACTCACCATCATGAGTCAGGTTGTGAAGACTAAG
AGCGTGGAGTACATGCCATTGCTGTTGTCGGTGGTGAGCTTCCTCAACGGCCTCTGCTGGACATCATACGCGCTCATCCG
CTTAGACATCTTCATCACCATACCCAATGGTCTTGGCGTGCTTTTTGCTCTCATGCAACTCATCCTCTATGCCATCTACT
ACCGAACCACACCCAAGAAGCAGGATAAGAACCTCGAGCTACCAACCGTCGCCCCTGTCGCTAAGGACACCAGCATCGTC
ACCCCTGTCAGCAAGGACGACGACGTCGTCGATGGCGGCAATGCCAGCCATGTCACCATCAATATCACAATTGAGCCATA
A

Alignment

ORF - retro_oind_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 89.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MISPDAARNVVGIIGNVISFGLFLAPVPTFWRICKRKDVEEFKADPYLATLLNCMLWVFYGIPVVHPNSI
          M.SPD..RN.VGI.GN.ISFGLFL.PVPTF.RI.K.KDV..FKADPYLATLLNCMLWVFYG.P.VHPNSI
Retrocopy MVSPDLIRNMVGIVGNIISFGLFLSPVPTFYRIIKNKDVQDFKADPYLATLLNCMLWVFYGLPIVHPNSI

Parental  LVVTINGIGLLVEGTYLLIFFLYSPNKKRLRMCAVLGVELVFMLAVILGVLLGAHTHEKRSMIVGILCVF
          LVVTINGIGL..E..YL.IFFL.S..K....M..VL..E..FM.AV.LGVLLGAHTH..RS.IVGILC..
Retrocopy LVVTINGIGLIIEAVYLTIFFLFSDKKNKKKMGVVLATEALFMAAVVLGVLLGAHTHQRRSLIVGILCAI

Parental  FGSIMYFSPLTIMGKVIKTKSVEYMPFFLSLVCFLNGVCWTAYALIRFDIYVTIPNGLGALFGAIQLILY
          FG.IMY.SPLTIM..V.KTKSVEYMP..LS.V.FLNG.CWT.YALIR.DI..TIPNGLG.LF...QLILY
Retrocopy FGTIMYSSPLTIMSQVVKTKSVEYMPLLLSVVSFLNGLCWTSYALIRLDIFITIPNGLGVLFALMQLILY

Parental  ACYYRTTPKKTKAAKDVEMPSV
          A.YYRTTPKK....K..E.P.V
Retrocopy AIYYRTTPKKQD--KNLELPTV

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_50 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA003951	1 retrocopy	retro_oind_50 ,
Oryza sativa japonica	OS01G0606000	1 retrocopy	retro_osat_38,