RetrogeneDB ID: retro_oind_5

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 11:13066549..13068841(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA034009
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA033375
• Aliases: None
• Description: None

Sequence

>retro_oind_5
ATGAGAGGCGCCGTGTTGGTGGCTGTGGCGGCCGCCATCGGCAACTACCTGCAGGGATGGGACAACGCCACCATCGCCGG
CGCCGTGCTGTACATCAAGCGGGAGTTCGCCCTCGAGACCCAGCCCGCCGTGGAGGGCCTCGTCGTCGCCATGTCCCTCA
TCGGCGCCACCATCATCACCACCTTCTCTGGCCCCGTCTCCGACCTCGTCGGCCGCCGCCCCATGCTCATCGCCTCCTCC
CTCCTCTACTTCGCCGGCGGCCTCATCATGCTCTGGTCCCCCAACGTCTACGTCCTCCTCCTCGCCCGCCTCGTCGACGG
CTTCGGCGTCGGCCTCGCCGTCACCCTCGTCCCCGTCTACATCTCCGAGACCTCCCCGCCGGAGATCCGCGGCCGCCTCA
ACACACTGCCGCAGTTCACCGGCTCCGGCGGCATGTTCATGTCCTACTGCATGATCTTCGCCATGACGCTCTCGCCCTCG
CCCAACTGGCGCATCATGCTCGGCGTCCTCTTCGTCCCCTCGCTGCTCTACCTGTTCGTCACCGTCTTCTACCTCCCGGA
GTCGCCGCGCTGGCTCGTCAGCAAGGGCCGCATGAAGGAGGCCAGGGTTGTGCTCGAGATGCTGCGCGGCCGCGAGGACG
TCTCCGGCGAGATGGCGCTGCTCGTCGAGGGCCTCGGCACCGGCGGCGACACCGAGATCGAGGACTACGTCGTCGGCCCG
TCCGAGGGCGACGCCGGCGAGAACGAGCAGGCGAGGGACACGGTCACGCTGTACGGGCCGGAGCAGGGGCTTTCGTGGGT
GGCGCAGCCGGTCGCCGGCGGCCGCGGCAGCATGCTGGGGAGCTCGCTGGGGCTGCAGGCGTCGCGCCACGGCAGCATGT
ACGAGCAGATGAAGGACCCCGTGGTGGCGCTGCTCGGGAGCGTCCACGAGCGGCTGCCGGAGTCCGGCGGCGGCGCCACC
GGCAGCATGAGGGGGAGCACGCTGTTCCCCAACCTCGGGAGCATGCTTAGCGTCAACGACAGGCCCGGCGGCAGCAGCTG
GGACGAGGAGAACGTGCAGCCTGGCGACGACGACCTCGACGAGGAGGAGGAGGAGTACCTCTCCGACGACGGCAAGGACG
ACGACGACGGCGGCGGCCTGCAGGCGCCGCTGCTGTCGCGGCAGAGCACCGACGTGGAGACCAAGAACGAGCCCGCCTCC
GGCCAGGTGGCGATGCAGCGGCACAGCAGCATCGGCGGCGGCGGCGGCGTCGAGACGGCGAGCACCATGGGCATCGGCGG
CGGGTGGCAGCTGGCGTGGAAGTGGACGGAGAACGTGGGCCCCGACGGCGTCAAGCGCGGCGCGGTGAAGCGCATGTACC
TGCACGAGGAGTCCGAGGCCGCGCCCGGCGGCGACGCGGGCGGCGGCGGCGCCGCCGGCGCCGCCGGCGACGCGCAGTCC
ACGGCGTACGTCCACGCGGCGGCGCTGGTGAGCCGGTCGATGCTGTACACCAAGGACGTCCTGATCGGGCAGAGCCCGAC
CGAGCCGGCGTTCGCGAACCCGCCGGAGGCGGTGGCGGCGGCGGCGTCGACGGGCCCGGCGTGGCGCGAGCTGCTCGAGC
CGGGCGTCCGCCACGCCCTCTTCTGCGGCGTCACCATCCAGATCCTCCAGCAATTCTCCGGCATCAACGGCGTGCTCTAC
TACACCCCGCAGATCCTCGACCAGGCCGGCGTCAGCGTCCTCCTCGCCAGCCTCGGCCTCTCCGGCGACTCCACCTCCAT
CCTCATCAGCGGCCTCACCACGCTCCTCATGCTCCCGTCCATCGGCGTCGCCATGCGCCTCATGGACGCCTCGGGCCGCC
GCGCCCTCCTCCTCTGGACGCTGCCCGTCCTCGTCGCGTCCCTCGCCGTGCTCGTGGTGGCGAACGTCGTGCCCATGGCG
GCGACCGCGCACGCGGCGCTGTCGACGGGGAGCGTCATCGTCTACTTCTGCTGCTTCGTCATGGGGTTCGGCCCCATCCC
CAACATCCTCTGCGCCGAGATCTTCCCGACGAGGGTGAGGGGACTCTGCATTGCCATCTGCTCGCTGACGTTCTGGCTCG
GCGACATCGCCGTCACGTACAGCCTCCCCGTCATGCTCAGCTCCGTGGGGCTCGCCGGCGTGTTCTCCTTCTACGCCGCC
GTGTGCTGCGTCGCGCTCGTGTTCGTGGCGCTCAAGGTGCCCGAGACCAAGGGCCTCCCGCTCGAGGTCATCATCGAGTT
CTTCAACGTCGGCGCCAAGGCCGGCACGTTGCCTGACGAAGAGTTCCACTGA

Alignment

ORF - retro_oind_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.19 %
• Parental protein coverage: 54.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAESQREGEDYGSDHGGDDIEDS-LQSPLISRQATSVEGKEIAAPHGSIMGAVGRSSSLMQGG--EAVSS
          D.....E.E.Y.SD.G.DD.....LQ.PL.SRQ.T.VE.K...A..G....A..R.SS...GG..E..S.
Retrocopy DDDLDEEEEEYLSDDGKDDDDGGGLQAPLLSRQSTDVETKNEPAS-GQV--AMQRHSSIGGGGGVETAST

Parental  MGIGGGWQLAWKWTEREGADGEKEGGFQRIYLHEEGVT---GDRRGSILSLPGGDVPPGGEFVQAAALVS
          MGIGGGWQLAWKWTE..G.DG.K.G...R.YLHEE......GD..G.......GD.......V.AAALVS
Retrocopy MGIGGGWQLAWKWTENVGPDGVKRGAVKRMYLHEESEAAPGGDAGGGGAAGAAGDAQSTA-YVHAAALVS

Parental  QPALYSKE-LMEQRLAGPAMVHPSQAVAK----GPKWADLFEPGVKHALFVGIGIQILQQFAGINGVLYY
          ...LY.K..L..Q....PA...P..AVA.....GP.W..L.EPGV.HALF.G..IQILQQF.GINGVLYY
Retrocopy RSMLYTKDVLIGQSPTEPAFANPPEAVAAAASTGPAWRELLEPGVRHALFCGVTIQILQQFSGINGVLYY

Parental  TPQILEQAGVGVLLANIGLSSSSASILISGLTTLLMLPSIGIAMRLMDMSGRRFLLLATIPILIVALAIL
          TPQIL.QAGV.VLLA..GLS..S.SILISGLTTLLMLPSIG.AMRLMD.SGRR.LLL.T.P.L...LA.L
Retrocopy TPQILDQAGVSVLLASLGLSGDSTSILISGLTTLLMLPSIGVAMRLMDASGRRALLLWTLPVLVASLAVL

Parental  ILVNILDVGTMVHASLSTVSVILYFCFFVMGFGPIPNILCAEIFPTTVRGICIAICALTFWIGDIIVTYT
          ...N........HA.LST.SVI.YFC.FVMGFGPIPNILCAEIFPT.VRG.CIAIC.LTFW.GDI.VTY.
Retrocopy VVANVVPMAATAHAALSTGSVIVYFCCFVMGFGPIPNILCAEIFPTRVRGLCIAICSLTFWLGDIAVTYS

Parental  LPVMLNAIGLAGVFGIYAVVCILAFLFVFMKVPETKGMPLEVITEFFSVGAK
          LPVML...GLAGVF..YA.VC..A..FV..KVPETKG.PLEVI.EFF.VGAK
Retrocopy LPVMLSSVGLAGVFSFYAAVCCVALVFVALKVPETKGLPLEVIIEFFNVGAK

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_5 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	BGIOSGA033375	1 retrocopy	retro_oind_5 ,
Leersia perrieri	LPERR10G13130	1 retrocopy	retro_lper_12,