RetrogeneDB ID: retro_oruf_17

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:7395160..7396936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G10010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI01G32100
• Aliases: None
• Description: None

Sequence

>retro_oruf_17
ATGGCCGCTAGAAGCGAGCTTCTCCGGCCGGCATTTGGTGAAGCATCTCCTTCGCTAGGACGGTTTGTCATCAACCCTCA
CAGCTGCAGCTACAGGTGGTGGCACATGTTCCTGATCATGCTGGTGTTGTACTCGGCATGGGCATCGCCATTCGAGCTGT
CCATGGAGAAGACAGCTTCCATTGCTCTTGTTGTCACAGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTA
TCCTTCTTCATCGCATACCGTGACACCTCCACCGGCCTCCTCATAACTGACCGCAGGAAGATCACAATGAGGTACCTGAA
ACGGCCGTGTTTCGCTCTAGATGTGGCCTCGACGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAG
GACTGTGGGGGCTCCTCAATCTTCTCCGTCTTTGGCGACTACGGCGCGTCAACAAGCTCTTTGCGAGGGTGGAGAAAGAC
ATCAGATTCAACTATTTGTGGACCAGGCTTATCAAGCTCCTCTGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCAT
CTACCTGTGGATGGCATTCAACTACAAGATCAAGGAACTTACATGGATAGGTAGCCAGATCCATAGCTTTGAGGACCGAA
GCGTGTGGTTTTGCTACACCTGTGCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTGCATGCC
ACCAACATTGGCGAGATGCTTTTCAGCATAGCCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACAT
CACTAACCTCGTTGTCCGTGAAACCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTCGGGAGCA
TGAACCGGCTGCCAGAGGCGATGAGGGAGCAGATGTTGGCCAGCGTGCAGCTCAGGTTCAGGACAGATGAGCAGCTGCAG
CAGGAGATGTTGTCAGAGCTGCCCAAGGCTGTGCGGTCGAGCGTCATGAAGCACATGTTCAAGAGTGCTATCGAGAGCTG
CTACCTATTCCAGGGAGTCTCCGACAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTCCCCCCCAAGG
CTAATGTTATCCTGGAGAATGAGACCTCGACGGACTGTTATATCATCATCTCTGGCGAAGTGGAGGCATTGACAACCCTT
GCAGATGGGACAGAGAAGCATGTGAAGAGAATAGGACCTCGGGGCATGGCAGGGGAAATCGGGGTGATGTTCAGCATTCC
GCAGCCATTCACCATCCGGAGCATGAGCCTCACCCATGTTGTCCGCATAAGCCATATCCATCTGCTCCAGGCTGTCCGGC
CTAACACCACAGATGGGTACATCGTGTTCTCCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTG
GCTTTTGTCAGCGATCATCTTTGGAATGGAAACTCAATGGTTTTGGGAAGGGCAACCGAGGTTGCTGTAGATGAATCAAA
AGAGGCCGCTCACAAAATGTTACCGTGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCA
CAACACTCCATCCTTCGCCTGGGAAGCTCGTCTTACTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAAAAGAAA
TTTGGGAAGGCCGTGAGAGGGATCCTCACTGTGGAAGGAGCCGAGGTCGAGGACATTGAAGTGATAAGAGATGGCGATCA
CCTGTTCTTTAGTTAG

Alignment

ORF - retro_oruf_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.94 %
• Parental protein coverage: 59.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQALYGLLNLLRLWRLRRVSKLFARLEKDIRFSYLWTRLIKLLYVTLFAVHFASCIYLWMAFHHKAKELT
          RQ.L.GLLNLLRLWRLRRV.KLFAR.EKDIRF.YLWTRLIKLL.VTLFA.HFA.CIYLWMAF..K.KELT
Retrocopy RQGLWGLLNLLRLWRLRRVNKLFARVEKDIRFNYLWTRLIKLLCVTLFALHFAACIYLWMAFNYKIKELT

Parental  WIGSQFHGFEDRSVWFCYTCAVYWSITTLATVGYGDLHAANTGEMLFSIAFMLFNMGLTSYIIGNITNLV
          WIGSQ.H.FEDRSVWFCYTCAVYWSITTLATVGYGDLHA.N.GEMLFSIAFMLFNMGLTSYIIGNITNLV
Retrocopy WIGSQIHSFEDRSVWFCYTCAVYWSITTLATVGYGDLHATNIGEMLFSIAFMLFNMGLTSYIIGNITNLV

Parental  VHETANTFKMRDMVQRTSVFGRTNRLPVAMREQMMESLQLRFRAEEQLQQEMLSELPKAVRSGIAQHMFR
          V.ET.NTFKMRDMVQR.S.FG..NRLP.AMREQM..S.QLRFR..EQLQQEMLSELPKAVRS....HMF.
Retrocopy VRETSNTFKMRDMVQRVSEFGSMNRLPEAMREQMLASVQLRFRTDEQLQQEMLSELPKAVRSSVMKHMFK

Parental  GAVQSCYLFQGVSDKLVLPLVAEMKAESFPPKADIILENEASTDCYIIVSGEVEVLTTLEDGTEKQVMRI
          .A..SCYLFQGVSD.L...LVAEMKAE.FPPKA..ILENE.STDCYII.SGEVE.LTTL.DGTEK.V.RI
Retrocopy SAIESCYLFQGVSDSLIVQLVAEMKAEFFPPKANVILENETSTDCYIIISGEVEALTTLADGTEKHVKRI

Parental  GPRGMAGEIGVMFNIPQPFTIRSRKLTQLARISHSHMVQTIRPNTADGVVVFSNFVLFTISHNV
          GPRGMAGEIGVMF.IPQPFTIRS..LT...RISH.H..Q..RPNT.DG..VFSNF.....S..V
Retrocopy GPRGMAGEIGVMFSIPQPFTIRSMSLTHVVRISHIHLLQAVRPNTTDGYIVFSNFIQYLESLKV

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_17 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17 ,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40,