Sequence
atgc intronic sequence ATGC exonic sequence...acaaacttcagggcattatcttctgttgaacaaactgagatcaaatattctttgcaatactacaaatcacccttctgaaaattttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
Basic information
species | Glycine max |
transcript | GLYMA12G29080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 3
------acaaacttcagggcattatctt---ctgttgaacaaactgagatcaaatattctttgcaatact-acaaatcacccttctgaaaattttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
|| | | | | | || || |||| | || | || | | || ||| | | || | | |||||||||||||||| ||||||||||| ||||| |||||||||||||||||||| | || | || || ||||||||||| |||| |||| | | | || |
gtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G11000.1 (Arabidopsis thaliana), 3'ss of exon 3
acaaacttcagggcattatcttctgttgaacaaactgagatcaaatattctttgcaatactacaaatcacccttctgaaaattttaataaatg-aatgc-agGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
||| ||| | | | | | | ||| | || ||| || | || ||| | | ||||| | | || ||||| |||||| |||||||||||| ||||||||||| || ||||| || | | |||||||| || || || |||||||||||||| || ||| | | || |||
--------gtaaatatttactttt-tctatcgacttaagagcctattttccttttga--cttttaattatattactgaactggatgttggatccaatgccagGGCCGTGAACCATTTGTGTCGTATGAGGGACTCGAGCAACTCCTAAGATTCTTATTCGTCCTGGGTATCACTCATGTTCTATACAGTGGCATTGCCATTG
upper sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 3
acaaacttcagggcattatcttctgttgaacaaactgagatcaaatattctttgcaatactacaaatcacccttctgaaaatt-ttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
| || | | | | | | | | | || || | || | | || ||| | | |||| || ||||||||| || ||| |||||||| | || ||||| |||||||| |||||||| | |||||||| || || || ||||| ||||||||||| |||| ||||
----------gtaaatccttctattcctgttacattatgttggggttttgatt-tggtgaaggaactagtagtactaaaagtcgtcgataatggattgcagGGCCGTGTACCGTTTGTTTCCCAAGAAGGTCTAGAGCAGCTTCACCGGTTTCTGTTTGTTCTTGGCATTACCCATGTCGTGTATAGTTGTATGGCGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctttgcaatactacaaatcacccttctgaaaattttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
ttttaat putative branch site (score: 3)
ttctgaaaattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaacttcagggcattatcttctgttgaacaaactgagatcaaatattctttgcaatactacaaatcacccttctgaaaattttaataaatgaatgcagGGCCATGAACCATTTGTTTCGTATGAGGGTCTTGAGCAGCTGCACCGGTTCTTATTTGTTCTCGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - -ggcatta
- - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - -ctttgca