Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgatcttgttacttgaaaaaaaaaagatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTATTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
----------------------------gtttgtg-atcttgttacttgaaaaaaaaaagatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTA-TTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
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cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccct-gctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
--------gtttgtgatcttgttac-ttgaaaaaaaaaagatgtaactttagggcttgatggtagttttata-acttgtagGA----GAATGTGCAGCAAG-TGTTGCTTA--------------TTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
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tcttttgaattttcaaactcattttgtttggtagatttatatacaacattctcttcatgtgatatttttatgcatttgattaatcttaactgcacaccagGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA
upper sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
--------------------gtttgtgatcttgttacttgaaaaaaaaaagatgtaactttagggcttgatggtagttttat--------aacttgtagGAGAATGTGCAGCAAGTGTTGCTTA-TTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
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atcaattacaggcattatatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
-------------------gtttgtgatcttgtt--acttgaaaaaaaaaa-------gatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTA-TTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
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ctatcaaatactgaaattatgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtttgtgatcttgttactt-----gaaaa---aaaaaagatgtaactttagggcttgatggtagt-tttataact--tgtagGAGAATGTGCAGCAAGTGTTGCTTATTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
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aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaaaaaaaaaagatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTATTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
ttataac putative branch site (score: 2)
aaaaaaaaagatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgatcttgttacttgaaaaaaaaaagatgtaactttagggcttgatggtagttttataacttgtagGAGAATGTGCAGCAAGTGTTGCTTATTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT