Sequence
atgc intronic sequence ATGC exonic sequencegtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
Basic information
species | Glycine max |
transcript | GLYMA12G33820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 4
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaat-gtctaatttgc-attgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
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---------------------------------------------------------------------------------------------------------------gtatgcaaaggatggcttttgacttctg---tatagttcagttcttg---tgcatttaataattttgtgcattgcaccaatttagGAAATCCAAGAGTGACACCAGAAGTCACAAGGGATGTATGCTTGCTTGCTAGAATGATGGCTTCAAATTTATACTGCTCGCAAATTGAGGATCTCATGTT
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 4
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctat-cttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
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----------------------------gtgagaaacatatctatt----ttgttgttg--gttcttagcactatgccttataa-----ataattacagcacaatgaatcct--ctttagatgttgtctttaaattactaccacttaggagataccatgtctgtatgcactctaaatttcaaatgacctttacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGATGTCTGCTTGCTTGCAAGAATGATGGCAGCAAACTTGTATTGCTCACAAATTGAGGATCTCATGTT
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
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-------------------------------------------------------------gtacatagcattctctctcc-----cttatttggatagtatatttgat----gtgctgaatcatgc-----aactgtagttcacaagaaagaagtgcaaatataactctgaa-----ctgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaa-atgttca-tatgtat-atctttttcaacttcagt--ttgggacactgcctcagagatgtggct-----tgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
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----------------------gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtct--ctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
gtctaat putative branch site (score: 3)
taatatacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctttcttttccctaagaaattaatgaaacaagcatttttattaacctctttgttacaattccttactttttgtccccaaatgttcatatgtatatctttttcaacttcagtttgggacactgcctcagagatgtggcttgtaatatacttattggtttctatcttacaaaatgtctaatttgcattgtagGTAATCCTAGAGTAACCCCTGAAGTTACAAGGGATGTGTGTTTGCTGGCTAGAATGATGGCTGCTAATATGTACTTCTCTCAGATAGAGGATCTCATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT