Sequence
atgc intronic sequence ATGC exonic sequencegttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
Basic information
species | Glycine max |
transcript | GLYMA15G16270.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 9
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcc-tattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
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--------------------------------gtatgtttactggttaatattact-catccctatcaccgttgaaattgacaactcaatcttatgcagAGGAACAAAGCACCAAATGAGCAAGCAATTCCCTTATTGATGCCTCAACATCACATGGTAATTCCCCATTACATGGGTAAAATCAAAGAATCAAATGAGG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 10
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
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----------------gtttgtctt----ttccattgcatactcatcatagtcttccccttc-attattgtaaataaaatacctttttttt---ccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCACCACATGGTAATTCCACATTACAAGGGCATAGGCCAAGAAATTAATAGTG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 10
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
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----------------------gttg----cttatatccttgtggtctgcttatcatag----aaagcggtaaacta-attgtttttttttctttcagAGGAACAAAGCTCTAAATGAGCAAGCAATTCCCTTACTGATGCCTCATTACCACATGGTAATTCCACACTACAAGGGTAGAAGCAAAGAAACAAATGATG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
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----------------gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtt--tttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 12
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
||| | | | | | |||| || | || ||| | || ||| | | | | || |||| | ||||| || ||||||||| ||||||||||||||||| |||||||||||||||| || ||||| |||||||||||| ||||||| ||||||||||| || |||
gttgatgtcttcactacatactccctagttcttctttcaaaagtataataaaccttttatctcaatacaagca----tacttttctg--------cagAGAAATAAAGCTCCAAATGAGCAAGCAATTCCACTACTTATGCCTCAGCAGCACATGGTCATTCCACATTACATGGGAAGGAGCAGAGAGATGGAGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
tattaac putative branch site (score: 1)
ttttttttatt CT-rich tract
tatattcccaaaatag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC