Sequence
atgc intronic sequence ATGC exonic sequencegttagacattcactgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04600.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 1
gt-tagacattcactgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttt-------taacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
|| ||| || | | || | | || || | | ||| || || |||| | ||| |||||| |||||| ||||||| |||||||| ||||| |||||||| | ||||| ||| | |||||||| || ||||| ||||||||||| || |||
gtacctccatccatttcctcccttctctccttcccttattttcttaaactataatttgatgatgtcgtttctttgtgtcgcagCGATTTCGCGGAGATTCTGGACGCGTATGAGAGGGGAGATAAGTTCTACTTGTACACCGGACGCGGACCTTCCTCTGAAGCCTTGCATTTGGGACACTTG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 1
----gttagacattcactgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
| | || || | || || | || ||| | | | || | | | ||| |||||| |||||| ||||||| || ||||| || ||||||||||| | ||||| ||| | |||||||| || ||||| ||||||||||| || |||
gtacctccatttcccccttcaccctttcctcgtttacttaaacggcgatttgatgatgtcgttttttttttgtgtccagCGATTTCGCGGAGATTCTGGACGCGTACGAGAGGGGCGACAAGTTCTACTTGTACACCGGACGCGGACCTTCCTCCGAAGCGTTGCATTTGGGACACTTG
upper sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gttagacattcac--tgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
| | | ||| | |||||| || | || | | | | | || | | ||| | || ||| | |||||||| |||||| ||||||| || |||||||||||||||||||| || | ||||| || ||||||||||| || || || ||||||||||||||||||
gtatgattgctttgtatatcattctttctcagtgtttttgtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
ttttaat putative branch site (score: 3)
ttgttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagacattcactgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC