Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
Basic information
species | Glycine max |
transcript | GLYMA17G03560.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgtt-atttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
| || ||| | |||| || || |||| | || | | |||| | |||||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||| | || |||
---------------------------------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgctcaa---cgctgttt----acatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 13
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcc-tgtttggtaaatttcac-cgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
| || | ||||| | | || | || || ||||| | | || | | | ||||| || | | | || | ||||||||| || ||||| ||||||||||| ||||| ||||||||||| || || ||||| || ||| |||| |||
------------------------------gtgagtataatgatattatttttcttcacttggttcgtctttgttagcctttcagcagtataacttgaatttgacatgatcactcccaccacgcagGACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcctgtttggtaaatttcaccgt--tttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
|| || | ||||| |||| | | | | | ||| | | | || ||| ||||||| | | | | |||| |||||||||| || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| ||||| | || |||
---------------------gtgagtttgtcatgcattctgttagctgtg-tagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
| || | | | || || || | || | ||| | || | ||| || | || || | || || |||||||||||||||| |||| ||||||||||||||||| |||| || ||| | || ||||| || ||| |||| |||
---------------------gtctggctgcaaactaacctctctccggtattgatcataggactttagattgtga--------gctttttttgtg--tgtctttgtgtgatgata-aatgcagGACATAAAACTTGCTGTTCATGCACATCCAACACTGTCTGAAGTTGTAGACGAACTGTTTAAAGCAGCCAAG
upper sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctc----aaagtctttcac-tgttatttatcctgcctgtttggtaaatttcaccgttttgtggta-caatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
||| ||| || ||| | || | | || ||| || | | | || ||| | | || |||||| | | ||| | | || ||| ||||| | |||||||||||||||| || ||||||||||||||||| | || ||||| || || ||||| |||||| |||| |||
gtaggatttcattgattagtgattactattgaatctagctcgtagcctttgatattgataatat-cctacagc-gaaatcaagtcatatacatagttcctgctgaaactactaaacgcattatttgtatctgtttcttgatcccctgcatgttttaatggtatctctgcagGACATAAAATTGGCAGTTCATGCACATCCAACACTCTCTGAGGTCCTCGACGAACTGTTCAAAGCAGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgttatttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
taaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgttatttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG