Sequence
atgc intronic sequence ATGC exonic sequencegtaacgcttttttgagtcttttatataagttgatgttgaagaaactggcagttcctataagctaaagatgatagtgttatgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 2
----------------gtaacgcttttttgagtcttttatataagttgatgttgaagaaactggcagttcctataagctaaagatgatagtgttatg-tttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
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tttgtgttgactagggacattgcaatgttatgttatttgtctt--ctgattttgtg--agcctcctgcatgggcatgatattctttgttgttttgtaacatcagGTACCATTGGGCATGTGGCCCATGGAAAGTCCACCGTTGTGAAAGCTATATCTGGAGTTCAG
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 2
--------------gtaacgcttttttgagtcttttatataagttgatgttgaagaaactggcagttcctataagctaaagatgatagtgttatgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
| | | || | ||| ||| |||| | | | |||| | | | | || ||| | ||||||| ||||| || ||||| || |||||||||||||||||||| || ||||| ||||| || |||
ttgtataactagggacattgtaatgttatattatttgcatat-ctgatttgtgaacttcctgcagcggcatgacattctttttcattctgtaaaatttcagGTACCATAGGGCATGTGGCCCATGGAAAGTCCACTGTTGTGAAGGCTATATCTGGAGTTCAG
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 2
-----gtaacgcttttttgagt--cttttatataagtt--gatgttgaagaaactggcagttcctataagctaaagatgatagtgtt----atgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
| | || | | | | ||||| || ||| || || | |||| | | || | | | || | ||||| |||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||
agcttcctatgaattcggaaatggcctgtatatgtattcagattttatgcgaaaggaggcctcctgtggtaccataatattttttctgcaaatatctcagGTACCATTGGCCATGTGGCTCATGGAAAGTCCACTGTTGTTAAAGCTATATCTGGTGTTCAG
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 2
----gtaacgcttttttgagt--cttttatataagttgatgttgaagaaactggcagttcctataagctaaagatgatagtgtt-------atgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
| | | ||| | | | | ||||| || | || || || | |||| | | || | | || || | ||||| |||||||| ||||| |||||||||||||| |||||||| || ||||| || || || |||
gcttattatggatttggaaatggcctgtatatgtattcaaattatgcgaaatgagaactcctgcgatagcataatatttttttttctacaaatatctcagGTACCATTGGCCATGTGGCTCATGGAAAGTCTACTGTTGTGAAGGCTATATCCGGAGTTCAG
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------------------------------gtaacgcttttttgagtcttttatataagttgat--gttgaagaaactggcagttcctataagctaaagatgatagtgtta-----------tgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
|| ||||| | | | | | || | || | | || | | || || ||| || | ||| ||||| | | | ||||||| || ||||||||||| |||||||| |||||||| ||||| |||||||| |||||||| |||
gtaattagcttatggaatgcttgaactaccttaccttagattagtcatcatatttactgcagaaggctttataaatccctgtctaggtgatggtcagctgtaaatcctaatcttttatatcagttgaagttgataatttcagttgattttatcttttcagGCACAATTGGTCATGTGGCTCATGGGAAGTCCACAGTTGTAAAAGCTATATCTGGTGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgaagaaactggcagttcctataagctaaagatgatagtgttatgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
agctaaa putative branch site (score: 3)
ttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgcttttttgagtcttttatataagttgatgttgaagaaactggcagttcctataagctaaagatgatagtgttatgtttcagGAACCATTGGTCATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA