Sequence
atgc intronic sequence ATGC exonic sequencegtgaatgattctatattttgagattattatagaagttttattgtaaataaaactaatggttctgataatattctcggttttctcattgtagCTGGACAGGAACGGTTTAGAACACTGACAAGCTCTTACTACAGAGGCGCCCAAGGAATCATTCTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03530.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G06780.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------gtgaatgattctatattttgagattattatagaa--gttttattgtaaataaaactaatggttctgataatattctcg-------gttttctcattgtagCTGGACAGGAACGGTTTAGAACACTGACAAGCTCTTACTACAGAGGCGCCCAAGGAATCATTCTCG
|||| ||| ||| | || | | ||| ||| | | |||| || || | ||| | | | |||| ||||||||||||| |||| ||||| || || || |||||||| ||||| || |||||||||||||| |
gtaatagttgctcgaatctttagcttctagttcatgagttggaccatttttaagttctgggttcatttgaattagatgcaaacaaatataatgaaatatttcttatag-ggtctttctgttgaatcactttccattgaccaaaatggttgattgaagtgttatattaataacattacatccatattgcagCTGGACAGGAAAGGTTCAGAACGCTAACTAGTTCTTACTATAGAGGAGCGCAAGGAATCATTCTTG
upper sequence: AT5G03530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g04740.t01 (Vitis vinifera), 3'ss of exon 2
-----gtgaatgattctat-attttgagattattatagaagttttattgtaaataaaactaatgg-ttctgat-aatatt--ctcggttttctcattgtagCTGGACAGGAACGGTTTAGAACACTGACAAGCTCTTACTACAGAGGCGCCCAAGGAATCATTCTCG
| | || | | |||| | || | | ||| | | || |||| |||| || | | || ||| | | || |||||||||||| |||| |||||| |||||||||||||||| ||||| |||||||| || ||||| |
atgttactagttatgttgtcatttcatgcttgtctcttttgcttttcta-gagcaatgtggatggattctcattagtcttaactcattatggctgatgcagCTGGACAGGAGAGGTTCAGAACATTGACAAGCTCTTACTATAGAGGTGCCCAAGGGATTATTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattgtaaataaaactaatggttctgataatattctcggttttctcattgtagCTGGACAGGAACGGTTTAGAACACTGACAAGCTCTTACTACAGAGGCGCCCAAGGAATCATTCTCG
ttctcggttttctc CT-rich tract
tgtaaataaaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatgattctatattttgagattattatagaagttttattgtaaataaaactaatggttctgataatattctcggttttctcattgtagCTGGACAGGAACGGTTTAGAACACTGACAAGCTCTTACTACAGAGGCGCCCAAGGAATCATTCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA