Sequence
atgc intronic sequence ATGC exonic sequencegtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g30540.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 15
gtgatcac---ttatct--gtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataa-gctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatg-tcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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gtgatcacaaattgtctcagtttactcagttacttagtttctcctcaattttaat--tgaatttgaatatgatgtgtctgctagtttgctgcataatgaccatacctatttactgcagtatccttttttatttaggttgaagcatgtc----tataattctca--ttttaatgctcaacagGTTGAACTATCTAATCCTGACGCTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 25
gtgatcacttatctgt---ttttccggtttatcca--ttctcttgcatcgt--ttatcctgaaaactgataacttggtgctatctattgagttctctct-tatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgt-caacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
|||||||| |||||| ||| || ||| | || || || || || || | | |||| | || ||| || | | || || || ||||||||| | |||| ||| | ||||| || ||| || || ||| ||||||| |||||||||||||| || ||||||||| |||| |||||||||||||||||||| || |||||||||||||||
gtgatcacaaatctgtcactttacccagttacttagtttgtcctgaattgtaattgaatttgattgtgatgtttctgt-tggtctggtgcataataactatacctatttactataatatcttttttttatgttgaagcatgtctataattctcatc-------------ttaatgttcaacagGTTGAACTATCAAATCCTGATACTGAGCTCCGCTTGCTTGAAGTATTTTACCACAAGATTTATAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 17
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatcca--atcctgatcttttaatgtcaac-agGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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--------------------------------------------------------------------------attttcctaataatat--tggcaaatt-ttctaacatgaataaattttaaaaataagtatactatatttctatatatcatgcccactttttactattgcttagGTAGAGTTATCTGATCCTGAAGCTGAACTTCGGTTGCTTGAAGTCTTCTATCACAAAATATACAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 6
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctg-atccaatcctgatcttttaatgtcaa-cagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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--------------------------------------------------------------------------attttcctaataatgttggcaacttttcctcca--ttaataaattttaaacgaaagtatactatatttctatatatcatgcccactttttactattgctcagGTAGAGTTATCTGATCCTGAAGCTGAACTTCGGTTGCTTGAAGTCTTCTATCACAAAATATACAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 21
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtc---aacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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--------------------------------------------------------------------------atatatggttttgggtcacattttggtggtaatgtatgctatgcagtt-gtgatttctgctt--tatggtaaatttgttaacattttttgttttgtgagacagGTAGATCTATCACATCCTGATGCAGAACTTAGATTGCTTGAAGTTTTCTATCACAAGATTTATAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 25
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttac-tataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
| ||| ||| || || || | ||| || || | ||| || | | | ||| || | | ||| |||||||||| |||| |||| |||| ||||| | |||||||||| |||||||||||||||||||||
--------------------------------------------------------------------------ttttataatactcttgtgcatgttcataggtccaagaacaatttttcagtagttgttgtggttaaaaacttactcctgtctggtgtgcattatgg-aacagGTTGAGTTGTCTCATCCAAATGCAGAACTTAGACTGCTTGAAGTTTTCTATCACAAGATTTATAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 25
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgat-ccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
|| || || | | ||| |||| ||| |||| | | | | |||| || |||| | ||| |||| | || ||| | ||||| | |||| || | | | | ||||| |||| || | | ||| | ||||||||| ||||| ||||| |||||||| | | ||||||||||| |||||||||||||| ||||||
--------gtaacttttctggcagttcatcc--cctcgatcatcttctgtacc-aaaattgtgcactttcttttattaattgttgcagcctttctctcccttctatagaat-ttttcttgtagttttgtaacgtctact----tgatgttgataccaaattttgga-----acagGTTGAGCTGTCTCATCCTAATGCTGAAGTTAGGTTGCTTGAAGTTTTCTATCACAAGATCTATAAG
upper sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 25
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattg--agttct--ctcttatcttgttact----ataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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gtatttattttactttttctttttatttgaaatttcttcggtgcacgatctcgtagtatcgcttcctcgatg-tgcatgttggtaattacagcacctgttctatcattctttacacgcagttactacttctgtattcatctcttgtgttgttgtgtttgtcttcatgtttt----tcga-agGTTGAACTTTCGAGTCCAAGAGCAGAGCTTCGCATTCTTGAAGTATTCTATCACAAAATTTATAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|25799966|gb|CA755927.1|CA755927EST: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAG GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTAT
genomic: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAGgtgatcactt ... atgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTAT
EST:
gi|58678315|gb|CK067002.1|CK067002EST: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAG GTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTAT
genomic: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAGgtgatcactt ... atgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTAT
EST:
gi|29637181|gb|CB642190.1|CB642190EST: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAA-CCAAG GTTGAACTGTCCAATCCTGATGCTGAAC
genomic: TACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAGgtgatcactt ... atgtcaacagGTTGAACTGTCCAATCCTGATGCTGAAC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
72 (upstream exon),
66 (downstream exon)
Score:
33GTTGTAATCCATAGCATAAGACTACCGAAAAACAGCACCATCAGTGATGTGATTACTGACCTAAAAACCAAGgtgatcactt ... atgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
ttttaat putative branch site (score: 33)
atcttttaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatcacttatctgtttttccggtttatccattctcttgcatcgtttatcctgaaaactgataacttggtgctatctattgagttctctcttatcttgttactataagctgttttatttttcatgaagagtgcctactatcctgatccaatcctgatcttttaatgtcaacagGTTGAACTGTCCAATCCTGATGCTGAACTCCGCTTGCTTGAAGTATTCTATCACAAGATTTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG