Sequence
atgc intronic sequence ATGC exonic sequencegtttctaaacttgctctgtcacattgtttaattttcaaacattgggggatggttaattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g14770.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------gtt-tctaaacttgctct-gtcacattgtttaattttcaaacattgggggatggttaatta-----------ttttatgcatgc-agGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
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gtatgtgctgtaacttcactatgattttgcataattattatcactgacaaattctaagtacagctgttgtttaatgttacttttatgttactatacaagtcacgt-tgttgagaaacacttcattcattagacaccttctcttgtatgttagATTGGGCTTCTCGAGTTTATTTTTCAGACAATGGATCTACTGCAATTGAAATTGCTTTGAAGATGGCATTTCGTAAATATGCATGTGACCATGGGATTAT
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G102156_T01 (Zea mays), 3'ss of exon 5
----------------------gtttctaaacttgctctgtcacattgtttaatttt-caaacattgggggatggt----taattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
| | | || | | ||| ||| |||| | | | | || || | | |||| |||||||||||||| || | || || ||||||||||| ||||| |||||||| ||||||||||||||||||| |||| | | |||||| ||
tttatttctttatttcttgcaactctatccacatcgctgatagcatcgttcctttttgcgtgcctatcatatttgtgtcacaacttcccctttttctcagGATGGGCTTCTCGAGTCTATTATTCAGACAATGGATCCACTGCAATTGAAATTGCTCTGAAGATGGCATTTCGTAAATTTTCTCTTGATCATGGAATTAT
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
--------------------gtttctaaacttgctctgtcacattgtttaat------tttcaaa--cattgggggatggttaattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
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gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgcatagtagctaactcattttt-tgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
upper sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
--------------------gtttctaaacttgctctgtcacat--tgtttaattttcaaacattgg--gggatggttaatt---attttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
|||| || | | | || | || || |||| ||| | || | | | |||||| | || | ||||||| |||||||||||| | ||| |||||||||||||| |||||||| ||| |||| | |||||||||||||| || || | | | |||||| |
gattttctggatttgttgaagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacattgtttaattttcaaacattgggggatggttaattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
ggttaat putative branch site (score: 4)
tttaattttcaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctaaacttgctctgtcacattgtttaattttcaaacattgggggatggttaattattttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG