Sequence
atgc intronic sequence ATGC exonic sequence...taaaatgtttaatttttgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26780.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 12
taaaatgtttaatttt--tgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
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aatgatagctaaatgtgctttgcagataaacttgtttttt--tttttcaaatttttatgccatatggggacaattatcatcctcttcaaatttcatgtttagGGCATAGATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAG
upper sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------taaaatgtttaatttt--tgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttg----cagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
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gtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatagGGGATAGATGGTTCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAG
upper sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 12
----taaaatgtttaatttttgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
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aaactgagataaatattgttcgcatataaaggatgggtataaattgtttt---tagcatgagaaatggaattaattatgtgttgt-ggaattttctttctacagGGTATTGATGGTTCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTG
upper sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------------------------taaaatgtttaatttttgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
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gtgtattctgcaaactcttcctcagtactgttatcacatgttccatgttctaattttctaccagtatgactattaattaagactgtgtcctgatctgcgatgaatggttcttgtca---------ttgtgtagGGTGTGGACGGTTCAAGGGTGGAGCGAGTGATGGAGCTTGCCCACATTGCAGCAAACAAGAACACTGTTCCAGGAGATGTGTCTGCATTGGTACCTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
taatttactcttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaatgtttaatttttgtactgttaaccttagtaggaagtgcttagaatagctaatttactcttgtaaaatatttgatgttggaaaatgggttttgcagGGAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCCTGGTGATGTTTCTGCCATGGTTCCCGGTG
- - - - - - - - - - - - -aacctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg