Sequence
atgc intronic sequence ATGC exonic sequence...cttcctaagcaagaagaaaatgcacatgtcatttgttagcatttgtgagttgagacaatggaacaatcttgacttatcttgcagtgtttttggttctcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
Basic information
species | Glycine max |
transcript | GLYMA02G48200.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G365185_T01 (Zea mays), 3'ss of exon 8
------------------------------cttcctaagcaaga--agaaaatgcacatgtcatttgttagcatttgt------gagttgagacaatggaacaatcttgactt---------atcttg---cagtgtttttggttctcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
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gtacgtataatgttctatgcctagttttagtttaccatgacatcttggcataagttcatgtgatctacaattagttgttctcaagaaccaagctagagtgtctttctaaaattgacgattcaatattaacaccatcttatctacttacagGTTTTTACTGCAGCTGCTGCTGATGATCGAAAAAATATTGTTTTGTTGGCATTTGAAACCATGGAAAAGATTGTTCGGGACTATTTCCCTTACATAACTG
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G38200.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------------------------------------------------------cttcctaagcaagaagaaaatgcacatg-----tcatttgttagcattt-gtgagtt----gagacaatggaacaatcttgacttatcttgcagtgtttttggttc----tcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
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gtacagaatgttttcctagcatctgcctgtatgtgaatatacagtatatgattaaggtttaagagaaaaaacgttcaacccaggatagaggatactatgcttagtagtttatctgctcgtgttttgttttttataagacacactctagtggtc--gacatgttttactgagtggccagtttcctttcagGTTTTCACAACTGCAGCAGCTGATGAAAGGAAGAACATTGTATTGTTGGCCTTTGAGACGATGGAAAAAATTGTCCGAGAGTACTTTTCATATATCACAG
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv03s0038g04090.t01 (Vitis vinifera), 3'ss of exon 8
cttcctaagcaagaagaaaatgcacatgtcatttgttagcatttgtgagttgagacaatggaacaatcttgacttatcttgcagtgtt-tttggttctcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
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-ctctagaccagctagctcatgtccatttgaatgcttaagaagtgggtaatgtggcccttgcaaatttcttgcttctcacatgatgctgttctatgttcagGTTTTTACGGCTGCAGCTGCTGATGAAAGGAAGAATATAGTCTTGCTAGCCTTTGAGACCATGGAAAAAATAGTGCGAGAATATTTCCCTTACATAACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagttgagacaatggaacaatcttgacttatcttgcagtgtttttggttctcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
tcttgac putative branch site (score: 3)
tgttttt putative PPT
ttatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcctaagcaagaagaaaatgcacatgtcatttgttagcatttgtgagttgagacaatggaacaatcttgacttatcttgcagtgtttttggttctcagGTTTTTACAGCTGCTGCAGCTGATGAGCGGAAGAATATTGTATTATTAGCATTTGAGACCATGGAGAAAATAGTGCGTGAATTTTTTCCTTATATTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
cttccta
- - - - gcaagaa
- - - - - - - - - - - -acatgtc
- - - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgga