RetrogeneDB ID: retro_olon_1

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538725.1:23410..24817(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538725.1_FG018
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538817.1_FG009
• Aliases: None
• Description: None

Sequence

>retro_olon_1
ATGGGGCGGTGTCTCCTCTGCCTCCTGCTGCTGCAGCTCGTGGGCCTCGTCGTCGCCGGCGGCGGGCGGTGGCGGTGGCA
GGAGGAGTTCCTCCGGCTGCCGGCGTCGGATGAGGCGACGAGGTGGGCGGTGCTGATCGCGGGGTCGAATGGGTTCTACA
ACTACCGGCATCAGGCGGACGTGTGCCACGCGTACCAGATCATGAGGAAGGGAGGCGTGGAGGAGGAAAACATCGTGGTG
ATGATGTACGACGACATCGCCCACAACCCCGACAACCCCAGGCCTGGCCTCATCTTCAACCACCCTTCCGGCCCCGACGT
CTACGCCGGCGTCCCCAAGGATTACACCGGCGACGACGTCAACGTCAACAACTTCCTCGCCGTCCTCCTCGGCAACCGCT
CCGCCCTCACCGGCTCCGGCACCGGCAAGGTCGTCTCCAGCGGCCCCAACGACCACGTCTTCGTCTACTACGCCGACCAC
GGCGGCCCCGGCGTCCTGAGCATGCCAGCCGACGGCGAGTACCTGTACGCCGACGACCTGGTCAAGGCGCTCAAGAAGAA
GCACGCCGCCGGCGGGTACAAGAGCCTGGTGGTGTACGTGGAGGCGTGCGAGTCCGGCAGCATCTTCGAGGGCCTCCTGC
CGGGCAACATCTCCGTGTACGCCACCACGGCCTCCAACGCGGAGGAGAGCAGCTGGGGCACCTACTGCCCCGGCGACGAC
CACGACGCCCCGGCGGCGGAGTTCGACACCTGCCTCGGCGACCTGTACAGCGTGGCGTGGATGGAGGACGCGGAGGCGCA
CCAGGAGGGGCGCCTCGCCGAGACGCTGCGGCAGCAGTACAGGACGGTGAAGAACCGGACGTCCGACGAGGGCACCTACA
CGCTCGGCTCCCACGTCATGCAGTACGGCGACATGGAGCTCGCACCGCAGAGCCTCGACCTCTACTACATGGACACATCA
CCTGCTGCTGCTGCTGCTGCCGGCGCCGGCGCCAAAGGCAGCCACTCCTACACTGTGTCTGTGAATCAGCGCGACGCCGA
TCTGCTCTACTTGTGGCGCAAGTACCGGAGAGCCGGCGAGGGGACAAGGCTTCTCCATCGGGAGCGGCTTGTGCAGGAGA
TGGGTCGGCGATCGCGCGTGGACAGAAGCGTGGAGATGATCGGGGGCCTCCTCTTGGGCGGCGCCAAGCACAAGCAGCAG
GTTGTGCGGGAGCGGGCTGCGGTGGTTGACGACTGGGAGTGCCTCAGGTGGATGGTGCGGACGTTCGAGGCTCAGTGTGG
GTCACTGGGGCAGTACGGGATAAAGCACATGCGCTCCTTCGCCAACATCTGCAACGCCGGCGTCCCCCACCACGCCATGG
CCAACGCCGCCTCCCTGGCCTGTCCATCCTCCCCGTTACACTTATGA

Alignment

ORF - retro_olon_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 70.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KADVCHAYQIMKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVYAGVPKDYTGKEVNVKNLFA
          .ADVCHAYQIM..GG...ENI.V.MYDDIAHNP.NPRPG.I.NHP.G.DVYAGVPKDYTG..VNV.N..A
Retrocopy QADVCHAYQIMRKGGVEEENIVVMMYDDIAHNPDNPRPGLIFNHPSGPDVYAGVPKDYTGDDVNVNNFLA

Parental  VLLGNKTAVKG-GSGKVLDSGPNDHIFIFYSDHGGPGVLGMPT-YPYLYGDDLVDVLKKKHAAGTYKSLV
          VLLGN..A..G.G.GKV..SGPNDH.F..Y.DHGGPGVL.MP....YLY.DDLV..LKKKHAAG.YKSLV
Retrocopy VLLGNRSALTGSGTGKVVSSGPNDHVFVYYADHGGPGVLSMPADGEYLYADDLVKALKKKHAAGGYKSLV

Parental  FYLEACESGSIFEGLLPNDINVYATTASNADESSWGTYCPG-EYPSPPPEYDTCLGDLYSVAWMEDSDVH
          .Y.EACESGSIFEGLLP..I.VYATTASNA.ESSWGTYCPG.....P..E.DTCLGDLYSVAWMED...H
Retrocopy VYVEACESGSIFEGLLPGNISVYATTASNAEESSWGTYCPGDDHDAPAAEFDTCLGDLYSVAWMEDAEAH

Parental  --NLRTESLKQQYNLVKERTSVQHTYYSGSHVMEYGSLELNAHHV-FMYMGSNPANDNATFVEDNSLPSF
          ......E.L.QQY..VK.RTS...TY..GSHVM.YG..EL........YM...PA...A.........S.
Retrocopy QEGRLAETLRQQYRTVKNRTSDEGTYTLGSHVMQYGDMELAPQSLDLYYMDTSPAAAAAAGAGAKGSHSY

Parental  SRAVNQRDADLVYFWQKYRKLPESSPEKNEARKQLLEMMAHRSHVDNSVELIGNLLFGSEEGPRVLKAVR
          ...VNQRDADL.Y.W.KYR...E........R..L...M..RS.VD.SVE.IG.LL.G...........R
Retrocopy TVSVNQRDADLLYLWRKYRRAGEGTRLLHRER--LVQEMGRRSRVDRSVEMIGGLLLGGAKHKQQVVRER

Parental  ATGEPLVDDWSCLKSM
          A.....VDDW.CL..M
Retrocopy AA---VVDDWECLRWM

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_1 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G093032	1 retrocopy	retro_zmay_6,
Oryza longistaminata	KN538817.1_FG009	1 retrocopy	retro_olon_1 ,
Oryza brachyantha	OB01G29280	1 retrocopy	retro_obra_23,
Oryza barthii	OBART01G19640	1 retrocopy	retro_obar_1,
Oryza glumaepatula	OGLUM01G23260	1 retrocopy	retro_oglu_32,
Oryza meridionalis	OMERI01G18100	1 retrocopy	retro_omer_24,
Oryza punctata	OPUNC01G20010	1 retrocopy	retro_opun_12,
Oryza glaberrima	ORGLA01G0161200	1 retrocopy	retro_ogla_9,
Oryza sativa japonica	OS01G0559600	1 retrocopy	retro_osat_9,