Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
Basic information
species | Glycine max |
transcript | GLYMA01G01270.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g44360.2 (Oryza sativa), 3'ss of exon 4
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaa-agttgaaatgcacatagtacataacttgggcttgatactgtaag-ctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
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-----------------------------gtaagtgcataa-catcatccttttctttcttcattttgaacaaacaaaataaaaggagttaaacgtttcag--tgatactgtttgtctggaaactgacctaataagataattatcattttgcagGTTATACTGGGAACACTTCTGGCAGCCTTAGTACCCGTGGTTGGTTTTAATGCAGTGATGACGTCTGAGCACTTTGCATCATTTCTG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G154165_T02 (Zea mays), 3'ss of exon 9
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG-------------
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-----------------------------------------------------------gtaagtccgtgggtttag-tgt-cataccaactcttttgtacaagtgaatactgaatagaa---aaaatttcataccggtaaacacaatgcagGTTGTGCTTGGAACACTTCTGGCAGCATCGGTACCTGTTGTTGGTTTTAATGCAGTAATGACGTCAGAGCACTTTGCATCATTTCTGGTATATTGATTGT
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 7
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
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-----------------------------------------------------------gtaagtccgtgggtttag-tgt-cataccaactcttttgtacaagtgaatactgaatagaa---aaaatttcataccggtaaacacaatgcagGTTGTGCTTGGAACACTTCTGGCAGCATCGGTACCTGTTGTTGGTTTTAATGCAGTAATGACGTCAGAGCACTTTGCATCATTTCTG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G060611_T01 (Zea mays), 3'ss of exon 9
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
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-----------------------------------------gtgagtgaataagcttcctctggttgg-----cgcaatcttctt----------tccagagtgttgtccagaactataacttaccagatcca-tggatcattt---tgtagGTTGTACTTGGAACGCTTCTGGCAGCATTAGTACCGGTGGTTGGTTTTAATGCAGTAATGACCTCTGAGCACTTCGCATCATTTCTG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
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-------------------------------------------------attagacaccaatgtttggttgccaggaaaaaaaatgtttcataactt---tttaacaaagaaatctcttttccttgtagtatttatagctttttcattgcagGTTGTGTTGGGAACATTGTTAGCAGCTTTGGTGCCTGTTGTTGGTTTCAATGCAGTAATGACATCAGAACATTTTGCATCATTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
acttgat putative branch site (score: 5)
ttttct CT-rich tract
taatttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatctgtttcagtcatacagttatgttagagtttaaataaaaacatttgcctttttcaattggaaagttgaaatgcacatagtacataacttgggcttgatactgtaagctgtaatttgaaatgtgcacttgattttctgaatgcagGTTGTATTGGGAACATTGTTGGCTGCCTTGGTGCCTGTGGTTGGGTTTAATGCTGTAATGACATCAGAGCATTTTGCATCATTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA