RetrogeneDB ID: retro_oind_42

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 1:28298304..28300572(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA004041
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA005797
• Aliases: None
• Description: None

Sequence

>retro_oind_42
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAAGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCCTC
TTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAGGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGAAGG
AGGAGAATAAGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGG
TACGCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACGGC
GCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGT
ACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCG
GTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAG
CACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACA
TGAGCACGTTCTTTGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCAC
GGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCG
CGACGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTGCTCTGCACCGTCCTCAGGT
CGGCGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATC
ACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCAT
CGCCAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCC
ACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTG
GTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCC
GAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGCAACT
ACGGCGCGTTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGC
AAGACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCAACGGCCGTGAACTA
CAACTCCTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACT
ACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACCGG
AGCATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGC
TGATAGCGTCTGCCCTGTTGTGTTATAA

Alignment

ORF - retro_oind_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 72.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNIVPVRL-TALH----EKDELPHGSRQ-ISRSKFFLVALICSFAWYAVPGYLFPTLTSISWVCWVFSKS
          G..V.V.L..ALH....EK.E...GS....S..KFFL.AL.CSF.WYAVPGYLFPTLTS.SWVCW.FSKS
Retrocopy GTLVQVSLFRALHGKGEEKEENKEGSGGGMSQAKFFLIALACSFLWYAVPGYLFPTLTSVSWVCWIFSKS

Parental  VTAQQLGSGLKGLGVGAFSLDWTAISSFLFSPLISPFFATANIFVGFVLFLYVLVPIAYWGFNLYNAKTF
          VTAQQLGSG.KGLG.GAF.LDWTA.S.FL.SPLISPFFATANI..G.VL..YV.VP..YWG..LYNA..F
Retrocopy VTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPLISPFFATANILAGYVLLMYVVVPVSYWGLDLYNARRF

Parental  PIFSSHLFMSNGTSYDITAIVNDKFELDIDAYNKLGRINLSVFFALAYGLSFATIASTVTHVGLFYGKEI
          PIFSSHLF...G..YDITAIVND.FE.D.D.Y...GRIN.S.FFAL.YGL.FATIA.TVTHV.LF.GKEI
Retrocopy PIFSSHLFTATGSTYDITAIVNDRFEIDMDGYHRMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEI

Parental  YHRFRASQKEKPDIHTRLMKKYDDIPVWWFYSLMALSMTVALILCTVLKHEVQLPWWGLLFACGMAFIFT
          Y.RFRASQ..KPD.HTRLMK.Y.D.P.WWFY...ALSM.V.L.LCTVL...VQLPWWGLLFAC.MAF.FT
Retrocopy YRRFRASQRDKPDVHTRLMKSYRDVPSWWFYAMLALSMAVSLLLCTVLRSAVQLPWWGLLFACAMAFVFT

Parental  LPISIISATTNQTPGLNVITEYAIGLIIPGHPIANVCFKVYGYMSMSQAIAFLSDFKLGHYMKIPPKSMF
          LPISII.ATTNQTPGLN.ITEY.IGL..PG.PIANVCFK.YGYMSMSQA..FLSDFKLGHYMKIPPKSMF
Retrocopy LPISIITATTNQTPGLNIITEYVIGLMLPGKPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMF

Parental  LVQFIGTIVAGTVNLGVAWWLLGSIHDICQDS-LPADSPWTCPNDRVFFDASVIWGLIGPIRIFGPHGNY
          LVQ..GT.VA.TVNL.VA.WLLGSI..ICQD..LPADSPWTCPNDRVFFDASVIWGL.GP.RIFGP.GNY
Retrocopy LVQLVGTVVASTVNLVVAYWLLGSIPNICQDALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNY

Parental  SALNWFFLIGAAGPVIVYIFHKMFPNKKWITLINLPVLIGATASMPPATAVNYNSWLLFGTIFNFFVFRY
          .A.NWFFL.GA.GPVIVY..H..FP.K.WI..INLPVLIGAT..MPPATAVNYNSWL..G.IFNFFVFRY
Retrocopy GAFNWFFLAGAVGPVIVYLLHRAFPSKTWIPMINLPVLIGATSYMPPATAVNYNSWLIIGIIFNFFVFRY

Parental  RKKWWERYNYILSAALDAGVAFMAVLLYFSLSMENRSIDWWGTAGEHCALATCPTAKGVDLGPTSVCPV
          RK.WW.RYNYILSAALDAGVAFMAVLLYFSLSMENRSI.WWGTAGEHC.LA.CPTAKG..LG..SVCPV
Retrocopy RKLWWKRYNYILSAALDAGVAFMAVLLYFSLSMENRSISWWGTAGEHCPLASCPTAKGINLGADSVCPV

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_42 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA005797	1 retrocopy	retro_oind_42 ,
Oryza nivara	ONIVA02G31600	1 retrocopy	retro_oniv_17,
Oryza sativa japonica	OS02G0695800	1 retrocopy	retro_osat_46,
Setaria italica	Si016420m.g	1 retrocopy	retro_sita_13,