RetrogeneDB ID: retro_oglu_35

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 3:8517294..8518257(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM03G11140
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM01G30530
• Aliases: None
• Description: None

Sequence

>retro_oglu_35
ATGTCAGTGCCTGTTTGCTCCCGCGACGACGAATCCGTGCCGACCTCGTTTCACCGCCTCCGCCTCCGATTCGACCTCCG
CGGCCGCCATGAAATTGGAGCTTCCGGGAGGAGGAAATCTCGAGAAGTAGAGAGAGAAGACCACAGCGTGGGCGAGCGCG
TCGGCGTCATTGATTCCGGCGACATGAAGCCCCCCGCCGCGGCCGCGGCCGGCAACAGGGCTGGTGGGGTGGATCCGTCG
ATACCGCGGTTCAAGTGCCAGGAGTGCCACCGCGCGCTCGTCGTCGTCGGCGTGGACTCCTTCGCCGCCGATAAGCTCCC
GGCTCAGGCCACCTCTGGGCATGTATCCTCTGTTCATGGAAGTATTATGGGAGCTAGCAGGATGGATAATTCTTATGTCG
TGCTATCCAAGCAAAACAAATCTCATGGCCATGGAATTCCCCCACGCCCACCGAGTGCAGCAGCCCCACATATCGAACCT
AACCAGCCAACAAGAGCGATGGAGGGTTCATATATAGTGCTTCCACCTGCTGCTGCTTCCATATACAAGACATCTACTTC
TGAAGGAGGTGGTGCGCAGTTGCCACCACCAAGTATCAATTCCAGCAGTTTGTTAACAGGAAATAGTTTTCACTCTAACG
TGACTGTATTAAAACGGGCATTTGAGATTGCTACGTCACAAACTCAGGTTGAGCAGCCAATGTGTCTGGGCTGTATGAGG
TTGCTCTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGACATTAAAGCTTATGAAGTTTGTCTTCAACATTT
GGAGCAGGAATCCTACAATGTCCTCAGCGATGCTGGTTTTCAGGAGGAGAAACTGAAGATTGAAGAAGAAGAAAAGAAGC
TTAACGCTGCTATTGAAGAAGCTGAAAAGCAATATTCAGAAATTAGTTCTGAGATGAAGGATCTTGAAATAAAATCTAAA
TAA

Alignment

ORF - retro_oglu_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.4 %
• Parental protein coverage: 54.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKAPAAAAAAVGNRAGGVDPSIPRFKCQECHRALVVVGVDSFA-DKLPAQATSAHASSVHGSIMGASRMD
          MK.PAAAAA..GNRAGGVDPSIPRFKCQECHRALVVVGVDSFA.DKLPAQATS.H.SSVHGSIMGASRMD
Retrocopy MKPPAAAAA--GNRAGGVDPSIPRFKCQECHRALVVVGVDSFAADKLPAQATSGHVSSVHGSIMGASRMD

Parental  NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGARLPPPSI
          NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGA.LPPPSI
Retrocopy NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPSI

Parental  NSSSLLPGNSFHSNVTVLKRAFEIATSQTQVEQPMCLDCMRLLSDKMDKEIEDVNADIKAYEVCLQHLEQ
          NSSSLL.GNSFHSNVTVLKRAFEIATSQTQVEQPMCL.CMRLLSDKMDKEIEDVNADIKAYEVCLQHLEQ
Retrocopy NSSSLLTGNSFHSNVTVLKRAFEIATSQTQVEQPMCLGCMRLLSDKMDKEIEDVNADIKAYEVCLQHLEQ

Parental  ESHTVLSDAGFQKEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSK
          ES..VLSDAGFQ.EKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSK
Retrocopy ESYNVLSDAGFQEEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSK

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_35 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM01G30530	1 retrocopy	retro_oglu_35 ,
Oryza glaberrima	ORGLA01G0218200	1 retrocopy	retro_ogla_19,
Oryza sativa japonica	OS01G0681400	1 retrocopy	retro_osat_20,