Sequence
atgc intronic sequence ATGC exonic sequencegtatagcttaaaagaatttgttttcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatttggttacactctttcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
Basic information
species | Glycine max |
transcript | GLYMA16G08510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 6
gtatagcttaaaagaatttgttttcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatt----tggttacactctt-tcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
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---------------------------------------------------gtctgctttttcgtgaacccccctcccttcttctattgccctcgctgcattaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G127754_T01 (Zea mays), 3'ss of exon 1
gtatagcttaaaagaatttgttttcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatttggttacactctttcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
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----------------------------------------gtctgttttttcgtgaacccttc----ctcccttcttctattgcccttgcttcattaacatccta-tgct-ttgtcgttggcagATATTTATACAAACTGGATATCCCCTTGAGTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------gtatagcttaaaagaatttgttt--tcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatttggttacactctttcaactgttatcatgctta---acagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
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gtggtacccaaactacagaaatcctgaactaattggcttaattctgtgtctgtttacattta-tcaaagacatagctaaggataggcccttaattatctttccttctgtctgaatttgtttaacagatatagtgatttcttgcagATATTTATTCAAACTGGGTATCCTCTAGACTTGCCGTCTGGGACTCTTGGGAGTTATTGCATCTATGAGTACCACATG
upper sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------gtatagcttaaaagaatttgttttcttgt-----ggttgttttctttaggtgtttaattgaaatat----ttatagttccacttgcctaaaacc---atttggttacactctttcaactgtt--atcatgcttaa------cagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
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gtgtatttatgcacataaactaccatgccttttatctatgtaacttgcatttttatctaatcttgtttgatattttttccccttttgtgttttttttatatgtgtacttatgattttggttggcattgattggaattctggaatgcccttttaatggtctgattttgctggagacgtgcagATATTTATTCAAACCGGATATCCTCTTGATTTGCCTTCTGGAAGTTTAGGAAGTTACTGCATTTACGAATATCATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccacttgcctaaaaccatttggttacactctttcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
gcctaaa putative branch site (score: 3)
ttatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagcttaaaagaatttgttttcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatttggttacactctttcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG