Sequence
atgc intronic sequence ATGC exonic sequenceGTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttg-tgtttgatatattaaaac-tcatgatgatgccatgtattcataggatttgttgatctgaatct---
|||||||||||||||||||| || || ||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||||||| ||||||||||||| || || | || | || | || | | || | || ||| ||| | | | | | |||| |||| | ||
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatga-----ctgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct--------------------------
|| ||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||| |||||||| || || || ||||| || || |||||||||||| ||| || | | | ||| | | | | | || ||| | ||| || || || | | | || | | |||| | |||
GTTTTTGACCTTGGGGGTGGAACATTTGATGTTAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgaga-attttttttttttatgagtcttaataagaagaacttattatgtagaaaaatat-attattctttccac-caaattctcctctgatgttaatgcttgctatgtctccttcgccttgccag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtgtttgatatatta-aaactcatgatgatgccatgtattcataggatttgttgatctgaatct------------------------------
|||||||| ||||||||||| || |||||||||||||||||||| |||||||| ||||| ||||| || || ||||| ||||| || || |||||||||||| || || | || | || || | ||| ||| || ||| || | || || || | ||| | |||| | | || ||
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagta----cttttatacac-atacacacaagctaatgtctgttattctatggaaatgaaattatataatct-ttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgat-gccatgtattcataggat-ttgttgatctgaatct-----------------
|| ||||||||||| ||||| || |||||||||||||||||||| |||||||| ||||| |||||||| || || || ||||| || || |||||||||||| ||| | | | | | | ||| | || || | ||| | || | | | | ||| | ||| || || | || |
GTTTTTGACCTTGGGGGTGGAACATTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagag-----atagctatcc-tatattattttcagatg----cttgtgtttgatatattaaaact-catgatgatgccatgtattcataggatttgttgatctgaatct-
|||||||| ||||||||||| || |||||||||||||||||||| |||||||||||||| ||||| || || || || ||||| || || |||||||||||| || ||| || | | | | | | ||| | | || | || ||| | | | |||||| | | | | |||| | |
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgcta-atgtctgctatttctgtttccccttactag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcc-----tatattattttcagatgc-ttgtgtttgatatattaaaact--catgatgatgccatgtattcataggatttgttgatctgaatct--------------------------------------------------------------
|| ||||| ||||||||||||||||||||||||||| ||||||||||||||||||| ||||||||||| || |||| ||||||||||| || | |||||||| | | | || | ||| |||| | ||| ||||||| ||| | | | ||| |||| || | | | | | | || ||
GTGTTTGATCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagaga-tagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct
|| ||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||||||||| || |||| ||||||||||| || | |||||||| | | | | | | || | || ||| || || | || || ||| | | | ||| | || |
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatga-attgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtg----tttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct--
|| ||||| |||||||||||||| |||||||||||||||||||| || || || ||||| |||||||| || ||||| ||||| ||||| ||||| ||||||||| || ||| |||| | | | || ||||| ||| | ||| | | | | | | | | |||| | | | ||||| | | ||
GTGTTTGATCTTGGTGGTGGTACATTTGATGTCAGTATCTTGACAATCGACAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagc-attgct-tccttggtccctaccttatttttgtgcattttttcctttgtaagattagttacggt-ttaaggattcttgg--tgtgttg-tagagacctct
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatccta-tattattttcagatgcttgtgtttgatatatt-----aaaactcatgatg---atgccatgtattcataggatttgttgatctgaatct---------
|| ||||||||||||||||| || || |||||||| |||||||| ||||| || ||||| || ||||| || || || ||||| ||||| ||| | |||||| || | | ||| | | | | || ||| || | ||| |||| | | || | | || | | | | | | |||
GTTTTTGACCTTGGTGGTGGAACCTTCGATGTCAGCATCTTGACTATTGACAATGGTGTTTTCGAGGTTCTTGCTACAAATGGAGACACTCATTTGGGAGgtgaggatttttttctctactgatgctctttcatctttgctctttgcacattgaaagaaaatttacgagaggaaagttattatactgtggatgctcaaggttcaattctttcctgcag
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgta----agagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct
|| ||||| || |||||||||||||| ||||||||||||||||| || || ||||| |||||||| ||| || | ||||| || ||||||||||||||||||| | ||| || | || ||| ||| | ||| || | || ||
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgatcaaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcag----------------------------------------
upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgta----agagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct
|| ||||| || |||||||||||||| ||||||||||||||||| || || ||||| |||||||| ||| || | ||||| || ||||||||||||||||||| | ||| || | || ||| ||| | | | || | || ||
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcag----------------------------------------Mapped 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|149067539|gb|EE157747.2|EE157747EST: CTGGCCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: CTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
EST:
gi|211197978|gb|FL446530.1|FL446530EST: GTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: GTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
EST:
gi|67031277|gb|CO460026.1|CO460026EST: TA-CGGTGTGTTTGAGGTGCTGGGCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCCAGAG-ATCATGGAATACTTCATCAAGTTTGATCA-
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACC-AGAGGATCATGGAATACTTCATCAAGTT-GATCAA
EST:
gi|67043231|gb|CO469486.1|CO469486EST: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCAGAGGATCATGGAATAC
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATAC
EST:
gi|32849239|gb|CD988920.1|CD988920EST: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
EST:
gi|211430777|gb|FL361062.1|FL361062EST: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAG GTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
genomic: TAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGA
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 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
198GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
Block sizes:
47 (upstream exon),
46 (downstream exon)
Score:
140GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
Block sizes:
45 (upstream exon),
47 (downstream exon)
Score:
174GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
761GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagata ... cttcattcagGTGAGGATTTTGACCAGAGGATCATGGAATACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCGGCAAGGACAACCGTGCTCTTGGAAAGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagagatagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG