Sequence
atgc intronic sequence ATGC exonic sequencegtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttctttttctgttgctgggattgttgtcatttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15220.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
-gtatctcgcctata-tactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttcttttt------ctgttgctgggattgttgtc-atttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
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gttatcttatagttactactcaaat-catttattat-gctttctgagttcatcctaacatatt-tcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
upper sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G36130.3 (Glycine max), 3'ss of exon 8
gtatctcgcctatatact--gagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttcttttt----ctgttgctgggattgttgtc-atttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
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gtatttt-tatagttactacaaaaatcatttatgttttctttgagttcatgctaacat-gtttctttttattctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATATGGTCTCTGGGCATTACTGCAATAGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
upper sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
gtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttctttttctgttgctgggattgt-tgtcatt-tagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
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gt-tgtaatatatttagtctaaatctcttttgttatgtttctctttggttctgttt---tttcacctttatttttagtttgttagtcattgtttttcttagaatc--atcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
upper sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 8
gtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttcttttt--ctgttgctgggat-tgttgtcatt-tagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
| | ||||| | || | | | | | | | | | || || | | | | ||| || | | | ||| | ||| || ||| | |||| | | ||| || |||||||||| ||||| || ||||| || | |||||||||||||| || || || || || ||||| ||||| || |||||||||||||| || || || |
----gttgta-atatatttagtctaaatctcttttgttatgtttctct-ttggttctgtttttccacctttattttcagtttgtgatagtcattggattttttagaatcatcactggagtattctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCGCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC
upper sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
gtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttctttttctgttgctgggatt---gttgtcatttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
| || || | | ||| || | | | || | || | | || | || ||| | | || |||| | || |||| ||||||||||| || |||||||| | ||||||||||||||||| || ||||| || || || || ||||| ||||||||||||||||| || ||||
---------------------------------tgaggtggtcagtatttgtgtttctccttttttgccatgttttgtccatttggtgcttcct-cccacttctgatattattgggccatgaacaatgatgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatatctaatattttttgccttctttttctgttgctgggattgttgtcatttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
atctaat putative branch site (score: 3)
tctaatatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctcgcctatatactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttctttttctgttgctgggattgttgtcatttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA