Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctcta--tgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
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------------------------------------------------------------------------------------gttcatatttttgcatatgattaaaaaggtgcaaatttgatattatatagctatattttttccttgaaa-attcatgaatatctt----tttgtaattattgcagGCGGTTGCTAATTCTACATCAGCAACATTTTTGCGTGTTGTTGGGAGTGAGTTGATCCAAAAGTACCTTGGTGATGGCCCCAAGCTTGTAAGAGAATTGT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgcct-tagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaac------ttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
| | | || | |||| | || || ||| || | | | ||||| | || || || | | | | | | || || ||| || | || | ||||| || ||||| | |||| || || || || || |||||||| |||||||| |||||||| ||||||||||| ||||||||| | || ||||| || || ||||| |||||| | |
---------------------------------------------gtttgcatttatctttgcttcttc-tagagctgtt------ttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgattt---aaggagtgttccagcatcttaagacaatgccttttgtgtatt-cagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcc-taaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
|| | | || | ||| || | || ||| | || || | | | ||||| |||| || | |||| || || | ||||||| || || || || |||||||| || |||||||||||||| |||||||| || ||||| ||| | || |||||||| |||||||| || ||| | |
----------------------------------------------------------------------------------gatccacat-ctcactgtgtcaactttgtttttattattgtgtatcgtgta---ctacacacagcacaatca-atttagtctaatacaaacccttttacttt-cagGCTGTGGCAAACTCAACATCAGCAACCTTTTTGCGTGTTGTTGGTAGTGAATTAATACAAAAATACTTGGGAGATGGTCCAAAGCTTGTAAGGGAACTTT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaact------tttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
|||| ||| | ||| | | | | | | ||||| | || || || | | | | || | || | ||| || | ||| | ||||| ||| |||| | ||||||| || || || || |||||||| ||||||||||||||||| |||||| |||| ||||||||| | || ||||| || || ||||| |||||| | |
--------------------------------------------------gtttgtgtttatcttttgcttcttctagagctgttttaatagagtttcaacatctcctttttactatctttatcttttggcagtgtttcaattt---aaggagtgtttcagcatcttaagactatgccttttgtgtatt-cagGCTGTGGCAAACTCAACATCAGCAACATTCTTGCGTGTTGTTGGTAGTGAACTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTAAGAGAACTTT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
|| | | | || || || | | | || | | || || | || | | || | ||| || ||| | | | |||| || || |||||||||||||| || |||||||||||||| || |||||| |||| || ||||| | || ||||||||||||||||| || ||| | |
----------------------------------------------------------------------------atggattgttgcagtgtgcctc-tttttaatgtgtctcttatgcttgttaaattcggaactgttggagatgag--caagtgttattt--------cttgttattctttcagGCAGTGGCAAATTCTACTTCAGCTACTTTCTTGCGTGTTGTCGGTAGTGAACTGATTCAGAAGTATTTAGGAGATGGTCCCAAGCTTGTGAGGGAACTTT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
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--------------------------------------------------------------------------------------------------------------------------------gtaagtgtgacatcttttaaggtgctgcttcg-taactaactagctttgg-ttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT
upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 2
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
| ||| | || | || || || |||| || || |||||||||| || || || || ||||||||||||||||||||||| || || | || |||||||| | || || ||||| ||||||||||| || | |
--------------------------------------------------------------------------------------------------------------------------------gtaaatgtgacatctttgaaggtgctacttcg--taattaactagctttggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCTMapped 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|71318158|gb|DR795841.1|DR795841EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTT
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTT
EST:
gi|148934976|gb|EC879019.2|EC879019EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCG-AAAG GCTGTTGCCCATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST:
gi|61117980|gb|DN558941.1|DN558941EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST:
gi|60357188|gb|DN224161.1|DN224161EST: ATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: ATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST:
gi|61117979|gb|DN558940.1|DN558940EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST:
gi|149110575|gb|EE190490.2|EE190490EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTG
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTG
EST:
gi|61117978|gb|DN558939.1|DN558939EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST:
gi|32831887|gb|CD971565.1|CD971565EST: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
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:
48 (upstream exon),
47 (downstream exon)
Score:
128CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
208CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
231CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
194CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
tttattcctaaaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT