Sequence
atgc intronic sequence ATGC exonic sequence...ccgacccgcttttttgtggatccagttacttcaatccggttgctgaattatataaccggaacaaaccaatttaaatcaaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------ccgacccgcttttttgtggatccagttacttcaatccggttgctgaattatataaccggaacaaaccaattt--------aaat--caaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
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gtgatgattctagggcagttttcttgagatctggtaacctgtgctctttggcttcacttgctcgaagtggtttcctgatgaacatgagagagaatgttgaaaaattcttgctgtgacggggttcaatggattaaagggctctctttttggtgttgagtgacaagaagtttgtggttgatttcagGTTGAATGCACAATTCCGAAAGATGATGGGACTTTAGCATCTTATGTTGGGTTTAGGGTCCAACACGACAATGCTAGGGGACCTATGAAGGGTGGAATCA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 1
---------------------ccgacccgcttttttgt--ggatccagttacttcaatc-cggttgctgaattatataaccggaacaaaccaatttaaatc--aaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| || ||||| | | ||| || | | | ||| | | | | | | | | | || || || | | | | | || |||| |||||||||||||| ||||| ||||| || | ||| | ||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||||
gcaagtaaaattacttcttgtgtttttcatttctttgttctggcaaaattagtttacttgttttcactgtactgtttcatatagttcaccaactctagctctaaatcatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACGTTGCAATCTTATGTTGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
----------------------------ccgacccgcttttttgtggatccagtt-acttcaatccggt-tgctgaattatataaccggaacaaaccaatttaaatcaaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| || || | | | |||| |||| | | | | ||| | ||||| | | | || || || | ||| | | || |||| |||||||||||||| ||||| ||||| || | ||| | || |||||||| |||||||| || ||||| ||||| ||||||||||| |||||||
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttc--acaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 2
ccgacccgcttttttgtggatccagttacttcaatccggttgctgaattatataaccggaacaaaccaatttaaatc--aaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
|| || || ||| | | ||| | | | | || | |||| | || | | | | || || || | | | || |||| || |||||||| || ||||| ||||| | | || | || ||||| |||||||||||||| || ||||| ||||| ||||||||||| || ||||
-tgatg-gcaccttgatggcttctgttttgttcttattttgtatttatcagataagcataaaatgcaactctagttctaaaacatgttgaatgaaaatgcagGTTGAGTGTACCATCCCCAAAGATGATGGAAGCTTGGCCACTTTTGTTGGATTCAGAGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGGATCA
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
ccgacccgcttttttgtggatccagttacttcaatc-cggttgctgaattatataaccggaacaaaccaatttaaatcaaccggttctgg-tatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
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--gtggtttctaatgatatgctcagttttctcatccatgataaccgtatgatttaccattttttgactatgctcttttcacttcttttgaacaaaattgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattatataaccggaacaaaccaatttaaatcaaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
atataac putative branch site (score: 3)
tattttt putative PPT
aaaccaatttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgacccgcttttttgtggatccagttacttcaatccggttgctgaattatataaccggaacaaaccaatttaaatcaaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
ccgaccc
- - - - - - - - - - - - - -acttcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaa