Sequence
atgc intronic sequence ATGC exonic sequence...agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
Basic information
species | Glycine max |
transcript | GLYMA04G09070.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
--------agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatg-ttgcattttg----aaatatagctaactcttat-------ttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
||| | | | ||| ||| |||| | || | |||||| ||| | | ||| || | | |||| |||| || || || |||||||| ||||||||||||||||||||||| || || | || ||| | | ||||| | ||||| |||||||||||| |||
----------gtaactcgacctgctcttcagat-gttccgtaagagtgtt-tcacatggcgtctctgaagt-tttagctaataaattttgtttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 6
agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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--gtgatctgctttctgttgttg--agatggaactttttttctta-tatggttgtttt-----aaaagtggatctcataag-atgcgtatatgac-acagGTATGTCCATGGTGATGTGAAGCCTGAGAACTTCTTGCTTGGTCCTCCTGGTACCCCAGAGGAGAAGAAGCTTTTTCTTGTTGACCTTGGATTGG
upper sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 6
agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
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--gtaattttctaatattt-ctgctac-tgtaactctctttcttcaagtggtttttatttgcta-agaagca----------gtgctcctgtttctacagATATGTGCATGGCGATGTAAAACCAGAGAATTTTCTGCTTGGGCCTCCTGGAACTCCTGAAGAGAAAAAACTTTTCCTTGTAGACCTCGGCTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
tcattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - -gcatggt
- - - - - - - -agcagca
- - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtc