Sequence
atgc intronic sequence ATGC exonic sequencegtaggttttaggtttcttcaatttcttgcttgttcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgggaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA13G38980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 2
-----------------gtaggttttaggtttcttcaatttcttgcttgttcatttgctt-cgtgctctgtgatttgaccgttgtggactgtttcgg-gaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
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gttagtggaatgtggaagtggaagcttgcaatccctaggct-ttgtttgttcggttgtttgctagtggtattattaggaatttgatcacgacgaaaacgaattgcagATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAG
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 3
gtaggttttaggtttcttcaatttcttgcttgttcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgg--gaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
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-----------gttggtgaaatgtgatgctttatt-tctgattcatcggttgtgccttgaagagtcagtaagggaaaagctgaattgcagATGGCTCTAATTGCTCGGCTGCAGCACCCTTACATTGTTGAATTCAAGGAGGCTTGGGTTGAGAAG
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 3
------------gtaggttttaggt--ttcttcaatttcttgcttgttcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgggaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
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gtcagcagaacagaaatttacacgccctttttcatttgtttgtttgtcattttgcactgtcttcggtgaactgataga-gcaaat------ggaaattgcagATGGCTCTTATTGCTCGCTTGCAACATCCTTACATCGTTGAGTTCAAGGAGGCATGGGTTGAGAAG
upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggttttaggtttcttcaatttcttgcttgttcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgggaattgt--agATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
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--------------------------gtaaaattcgaatcatttgaatttcgagatttcgataaggactaacattggtgaaattctctagATGTCTTTGATTGCAAGAGTTCAACATCCTTATATTGTGGAGTTTAAAGAAGCTTGGGTTGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgggaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
atttgac putative branch site (score: 4)
aattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttttaggtttcttcaatttcttgcttgttcatttgcttcgtgctctgtgatttgaccgttgtggactgtttcgggaattgtagATGACTCTTATTGCTCGAATTCAGCATCCTTACATTGTGGAATTTAAAGAGGCTTGGGTTGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG