Sequence
atgc intronic sequence ATGC exonic sequencegtggtatttttgtatggaattagttttgttctttatgtcactatttgatagtatcctacaaatatgcaaatgcaaaaagatggctttatggaacctaactgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36390.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 13
gtggtatttttgtatggaattagttttgttctttatgtcactatttgatagtatcctacaaatatgcaaatgcaaaaagatggctttatggaaccta-actgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
| ||||| || || | ||| ||| || |||| | ||| | | ||| | | | | | | | |||||| | ||||||||| |||||||||||||| ||||| | | | ||||||||||| |||||||| || || |||||| || ||| | ||||||||||| |
--------------agcgattagccctgcaaagagtgcaaag----gattatatttcactcatattctttctcaatcatttaattttttttcttttgcattattgaatctcgctgcagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGGTTTACCTGATGCTGACTAATGATGTCATTCATGGGCTCT
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 13
gtggtatttttgtatggaattagttttgttctttatgtcactatttgatagtatcctacaaatatgcaaatgcaaaaagatggctttatggaacctaactgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
| | | | || |||| || | | ||| | || | |||| | ||| | | ||| | | | | | | |||| | ||||||||| |||||||||||||| ||||| | | | ||||||||||| |||||| | || || |||||| || ||| | ||||||||||| |
--------------tagcagtgatt--agcctttgaatcgaaagattatatttcact-tagatattctttctcaatcatttaatttttttcttttgcattattgaatgtgactgtagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGATTTACCTGATGCTGACTAATGATGTCATTCATGGGCTGT
upper sequence: AT2G36390.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 13
gtggtatttttgtatggaattagttttgttctttatgtcactatttgatagtatcctacaaatatgcaaatgcaaaaagatggctttatggaacctaactgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
| || | | | | ||| | ||| | | |||||||| ||| | | | |||| | || ||| | | || | || || || |||| ||||||||||| || ||||| || || ||||||||| |||| ||||| || || |||| ||||||||||| || || ||| | ||||||||||| |
----tgttact-tgggttgctgaggttgcgttctatatgaatatttgattctatgtt---------ctactgcagcctg--ggtcttacagcatttatttatgtgc-ttgctgttagGTAGAATTTACTGGAAACTACAACGAATATTTTGGATATGCTACCGATGTAGATGCCATGGTTTATCTAATGCTCGTTAATGATCTTATTCATGGGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcaaatgcaaaaagatggctttatggaacctaactgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
acctaac putative branch site (score: 2)
aaaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggtatttttgtatggaattagttttgttctttatgtcactatttgatagtatcctacaaatatgcaaatgcaaaaagatggctttatggaacctaactgctagcgtttgtggcagGTCGAATTTACTGGGAATTACAATGAGTACTTTGGATATTCTACTGATGTTGACGCTGTGGTCTATCTAATGCTGGTGAACGATTTGATTCATGGGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG