Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
Basic information
species | Glycine max |
transcript | GLYMA15G12790.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggtattctaatat-tagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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-----------------------------------------------------------------------tttcttcagaaacatatgaacaagtaccacaataatgtgatttg-------------catt------tcttgatgta-gtgcttttcattgt-tgaatcttacactcacaaatgtgtgcagTTGGTGATCATGGTGTCAAGGCACAAGGTGATGGATGGTTGTTAACAGTTGCCTTAATTGAGGGAACCAAACTGGCTCCAGTTGATGCTACTGGTTTTTC
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g10630.1 (Oryza sativa), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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-------------------------------------------------------------------------------gaaaaaaaactgtattcacctaagaattgacttttcctgttcttggg---gataaatcata--aatgacaa-------gcatatgtaacctttttccctcttccaatattagGTAGTGATCATGGGGTGAAAGCTCATGGTGATGGTTGGTTGCTGACTGTTGCACTTATTGAGGGAAGCGGTGTAGTAGGTTCAGGTACACCTGGCTTGCC
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccat--gtttttaattatattgacctttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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------------------------------------------------------------------------------------ctttagaaaaaccttctattcttgt--tctggacatatatactcccgtgatttatgcacatatgaactaaactttgcttacatgg---tatttgggagtata----tagGAAGTGATCATGGAGTCAAAGCACAAGGGAATGGTTGGTTGCTGACTGTCGCTCTGATTGATGGTACCAATTTAGCAGCAACCAAATCATCTGGTTACTC
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G005195_T03 (Zea mays), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacc--tttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC---
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-------------------------------------------------------------------------------------------tttatttttctttgattcaacaaaact-tccaggtttcagatactgttctggataattactcttacaatcttccttattgatcttttggattgta-tattagGT---GATCATGGAGTCAAAGCACAAGGGGATGGCTGGTTGCTGACTGTTGCTCTGATGGAGGGAACCAACTTGGCAGCAACCAAATCATCTGGTTACTCTGA
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttg-gt--attctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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---------------------------------------------------------------------------------gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgttta-tccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
upper sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggta--ttctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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----------------------------------------------------------------------------------------aaaaaatattgccatattattttctcaaatctgttat-tttattggttttttct--tcttgttggtttaaa--attttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttaatgcccatgtttttaattatattgacctttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
ttctaat putative branch site (score: 2)
tttttaattatattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggtattctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA