Sequence
atgc intronic sequence ATGC exonic sequence...gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactattatttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G146378_T01 (Zea mays), 3'ss of exon 1
gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactattatttattccatttcgtccaa--tataact----ctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
| || | || | | | ||||||||| || | | ||||| ||| ||| || | | ||||| | || ||| | ||| | | | ||||||||||| ||||| ||||||||||||||| |||| ||| | || ||||| |||||||||| ||||| || ||||| || || ||
-----tctgcttaacataatgcaatgatacttttgaaaaggttgctcttttatgtattagttagatcataaggtgatatttgtaactgatgttctgctgctgc-agGAAAGCGATTCTTTGAAGAGTTAGACAGAGATGGTGATGGCCAAGTCACTCTAGAAGATCTCGAAATTGCAACGAGGAAGAGGCGGTTGCCAAGGAGGTA
upper sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G003033_T01 (Zea mays), 3'ss of exon 1
gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtac-tattatttattccatttcgtccaa--tataact----ctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
|| | || | | | ||||||||| || | | || ||||| || ||| || | | ||||| | || ||| ||| | | | ||||||||||| || || ||||||||||||||| |||| ||| | || ||||| |||||||||| ||||| || || || || || ||
------ctgcataacataatgcaatgatacttttgaaaaggttgctatttttatgtattagttggatcataaggtgatatttgtaactgatgttctgctgctgt-agGAAAGCGATTCTTTGAAGAGTTGGACAGAGATGGTGATGGCCAAGTCACTCTAGAAGATCTCGAAATTGCAACGAGGAAGAGGCGGTTACCAAGGAGGTA
upper sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G35730.1 (Glycine max), 3'ss of exon 2
gctaa--tatg-aggaccacgttact-tatttgcttttgaaatttttacgtcctgtactattatttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
|||| |||| |||| | | |||| || || | || || | | | ||| | || || | | || | | ||| | | | | |||| |||||||||||||| || || ||||||||||| |||||| |||||||| |||| ||||| ||| |||||||||| | |||||| |||| |||||||
-ctaaactatgtaggaactggctactgtacttacaatttaagtcctctt-tgtggtattggctggaatgacaaat--ttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
upper sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G31800.1 (Glycine max), 3'ss of exon 2
---gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactatt-atttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
|||| |||| | || || | ||| || | | ||| |||| | | | || | | ||| | | | | |||| |||||||||||||| || || ||||||||||| |||||| |||||||| |||| ||||| ||| |||||||||| | |||||| |||| |||||||
ctaaactatatagggactgactactgtacttacattttaagtcatc----tttgtggtatttgctggaatgacaaatttcactgtcactttcattatcatacagGGAGGAGGTTCTTTGAGGAGTTGGATAGAGATGGGGATGGCCAAGTAACTCTGGAAGATCTAGAAGTTGCAATGAGAAAAAGAAAGCTGCCACGAAGATA
upper sequence: AT2G35800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g03870.t01 (Vitis vinifera), 3'ss of exon 1
----gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactattatttattccatttcgtccaatat--aactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
|| | | || | || | ||||| |||| || | | ||||||| ||| || || | || || | ||| ||| ||| ||||||||||||| | ||||||||||||||||| ||||||| ||||| ||||| ||| | |||||||| || |||||| |||| | |||||
gtttactctttttgggctggttatgctccatcactttt---tcttttgtttctt---caattatttgcaaggtttattctcattttgaaatcatgcattcttatagGAAGGCGGTTCTTTGAAGAGCTGGATAGAGATGGTGATGGTCAAGTAACATTGGAAGATCTTGAAGTCGCAATGAGAAGCAGAAAACTGCCACGGAGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcctgtactattatttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
atataac putative branch site (score: 3)
ctctttgt CT-rich tract
tattatttattccatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctaatatgaggaccacgttacttatttgcttttgaaatttttacgtcctgtactattatttattccatttcgtccaatataactctttgtggcttccagGCAGGAGGTTCTTTGAAGAATTAGATAGAGATGGTGATGGCAAAGTAACTTTGGAGGATCTGGAAATTGCAATGAGGAGAAGAAAATTGCCCAGAAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctttg