Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcaccaataaatctgcgatgctcataccagcatttccctgtggtttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04360.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G158043_T01 (Zea mays), 3'ss of exon 19
----------------------------------------------------------------------gtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcacc--aataaatctgc---gatgctca--taccagcatttccctgtgg-tttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
|| || || || | ||| ||| || | || | | | ||||| | ||| ||| | | || |||||||| || |||| |||||||||||||||||||| || ||||| ||||| ||| | |||
gtaaatttctgaagttttttttttaaaaactgtacgtattaaatcgtcaaagctcacactctggaagagcataatatgttttctgattaggatggccataattgaattacttttttttccttatttactctgctaaaaaaatcagttactgatacattttcatgaatttcagATAAACTACGCCTCTGCTCATGACAATGAAACACTATTTGATATTATTAGTCTAAAG
upper sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G34080.1 (Glycine max), 3'ss of exon 20
---------------------------------------------------gtatgcaacttcctttctatcactttcatcatttaagtga-----aacaagcaccaa----taaatctgcgatgctcataccagcatttccctgtggttt-cagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
|||| | ||| || | | |||||| | | | | || || | || | | ||| || | | |||| | || ||| ||||| ||||| || |||||||||||||||||||| || ||||||||| | || || |||
gtaagcttattcacttatatattcctcaactgttcttcctcttaaatctaaacatgctctgtattttgagaaacatcaagaatttaaattatcagtattgaacatcattttttgaaccagagatcatctaatcggcatctttagatgttttgcagATCAATTATGTTTCTGCTCATGACAATGAAACCCTATTTGACATTGTGAGCTTAAAG
upper sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ37579 (Selaginella moellendorffii), 3'ss of exon 19
gtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcaccaataaatctgcgatgctcataccagcatttccctgtggtttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
| || |||||| | | | | || | || ||||||| || || |||||||||||||||||||||||||||||||| |||| |||||
-----------------------------------------gtatgc-ttgataaatgtatttctgtttgcctactgattttgcatt-ttgtagATTAACTATGTCTCTGCTCATGACAATGAAACTCTCTTTGACATCATCATGATGAAG
upper sequence: AT5G04360.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ34076 (Selaginella moellendorffii), 3'ss of exon 19
gtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcaccaataaatctgcgatgctcataccagcatttccctgtggtttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
| || |||||| | || | | || | || ||||||| || || |||||||||||||||||||||||||||||||| |||| |||||
-----------------------------------------gtatgc-ttgataaatgtatttctgtctgcctactgattttgcatt-ttgtagATTAACTATGTCTCTGCTCATGACAATGAAACTCTCTTTGACATCATCATGATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaagcaccaataaatctgcgatgctcataccagcatttccctgtggtttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
tttccctgt CT-rich tract
aataaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaacttcctttctatcactttcatcatttaagtgaaacaagcaccaataaatctgcgatgctcataccagcatttccctgtggtttcagATTAATTACGTATCTGCTCATGACAATGAAACTCTCTTTGACATTATCAGTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG