Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctaaaatttgtaccctctttggtgatgatgggtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G59110.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 4
-----------------gtaagtctaa--aatttgtaccctctttggtgatgatgg-gtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT-
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tatgcacatgtttcagtatctacttgactactttatagattttatttaaaggattgcataaatagaaacttattcctattggacctgttccca-atttcagtTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTAGAAGCAGTTACTGGAAAGGATC
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
-------------gtaagtctaaaatttgtaccctctttggtgatgat-gggtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
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gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaatagaaacttactcatgttggacctgttccca-atttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 4
gtaagtctaaaatttgtaccctctttggtgatgatgggttttt-gtatacatattattaacgg-tcatgtgtatat---gcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
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gtatacagaaaatttattatctctttccttattttatacttaaaggatttgtacacttaggaactcacttttgttttggatttcagTTATGTGGCACCAGAATATGCTAACAGCGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTGCTGGAAGCAGTTACTGGAAGGGAC
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
gtaagtctaaaatttgtaccctctttggtgatgatgggttt-----ttgtatacatattattaacggtcatgtgt-atatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
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gtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcac-ttaggaactcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtaagtctaaaatttgtaccctctttggtgatgatgggtttttgtatacatattattaacggtcatgtgta---tatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
| ||||| | | | || | | |||| ||||| | | | | | | ||| | | | |||| ||||| ||||| |||||||||||||| || | || |||||||||||||| ||||| ||||||||||| || ||||| || | | |||||||| |||
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgatgatgggtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
tattaac putative branch site (score: 1)
tttttgtatacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctaaaatttgtaccctctttggtgatgatgggtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
