Sequence
atgc intronic sequence ATGC exonic sequence...atttagttttgcatattttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
Basic information
species | Glycine max |
transcript | GLYMA09G01050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 6
-atttagttttgcatat--tttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
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taggacattttgcacataatatgaaaatcatcacggcaataataacaagttg-acgatttttcctcaaaaaagttaacgattgatccatcttcttt--ttcagATATACTCTGAAATGATTGGTAATGTTATGACTGATGCACGCTCAACCGGGAAGTACTACCACT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------atttagttttgcatattttct---atacccttttagttttagat----acatggtgcatgattacat-----gact--tgattgttttcctatgtttatgt-taatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
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gtatctaattcttgattgttgactatgtatgaagtctcagtctaggtttttaattagctacaatggtgatgggctaattgctcaccgcacacctgctcgagcattctttcaatttgaaattaaggcattctacacagatgcatttgaaaacccatcatgaatatatcatgacaaggaatcatatttttcagATATACTCTGAAATGATTGGCAATGTTATGACTGATGCGAGATCCACTGGAAAATACTACCACT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 6
atttagttttgcatattttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgta-atgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
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-----------------gtaagtaactttaaaattt---atgcataactta-gttgtctttttatagaagaccttccat-tttgtgattatatacatgtagATATACTCAGAAATGATTGGAAATGTTATGATCGATGCGCGTTCCACGGGAAAATACTATCACT
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 6
---attta-gttttgcatattttctatacccttt-tagttttag--atacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
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atcatccatgtgactaatggttgaaatgcctcttatggttgcagtagtaagttttgcattgtaaaataatc--aatggtatgttgtattt---ttaacc--atgcagATTTATGCAGAAATGATTGGGAATGTCATGATAGATGCTCGCTCAACTGGAAAATACTATCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
tgttaat putative branch site (score: 3)
tttatgttaatgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttagttttgcatattttctatacccttttagttttagatacatggtgcatgattacatgacttgattgttttcctatgtttatgttaatgtaatgcagATATATTCTGAAATGATTGGAAATGTTATGATAGATGCCCGATCAACTGGAAAATATTACCATT
- - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgac