Sequence
atgc intronic sequence ATGC exonic sequencegttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtctt-gttgcataatttatgttaagctatctgttatctactcttttttgctgttt-ttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
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------------------------------gttacat--ggtcacatacctttttactcacta---gagctgtttttatttaacatgtt-tacaaatcttagttg------ttaggtcagatctcct--tgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgttt-ttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
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gtaacatggtcacatctattactgtttt--tgtttttca---ctagttctgttt--------ttatttaacatgtttac-----aaaatattagt----tgttacttg--ttaggtacagacttccttgatg-attcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataattt-atgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA-
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--------------------------------------------------------------------------aatat-taatcaagctatcatattctttatcagagtttgatgttaa--tagctaccattcaatggatttt--tgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
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----------------------------------------------------------------------------gatcttttcgtaggttatgattataaatca-agctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
||||| ||| || ||| || |||| | || ||| | | ||||| || || | ||| |||| || | | | | || |||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||| | || || || || |||||||| ||| ||||||| |
----------------------------------------------------------------------aattttaatc----aagctatcattttctttatcagattttgatggttaa-tatctaccatttaatggattt--gtgttgctgattcttatgtaatacttgttgcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
gttacgaagcttc--ctctattgcaattt-tgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaat--attcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatc--tttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
|||| | | | || | | | | || | |||||| || || | | |||| || | | ||| || || | | || || | || | ||| || | | ||||| ||| | | | || || | || |||| |||| |||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||| |||| ||||| || || || || ||| |||| || |
gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
upper sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttc-cacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
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--------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgctt---ttcagtttttatgcatgttgtatact-tcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCAMapped 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|78107197|gb|DV525615.1|DV525615EST: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCCACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST:
gi|71439100|gb|DR820150.1|DR820150EST: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
EST:
gi|5847365|gb|AW000444.1|AW000444EST: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAG TTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: ATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
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:
45 (upstream exon),
47 (downstream exon)
Score:
52ACGCTGACGTACGGTTAACAAGGAGGATCCATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
52ACGCTGACGTACGGTTAACAAGGAGGATCCATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
72ACGCTGACGTACGGTTAACAAGGAGGATCCATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
Block sizes:
48 (upstream exon),
45 (downstream exon)
Score:
146ACGCTGACGTACGGTTAACAAGGAGGATCCATCGTGATACCATTGACAAGGGTAGAGATCTCAAAGCTGTGTTAGAACAGgttacgaagc ... ttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
ggctaac putative branch site (score: 146)
tctttttttccac putative PPT
taacaaatcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA