Sequence
atgc intronic sequence ATGC exonic sequence...gtgttgtgctcttacttctagacatctcaaaatcctacattggttacagttcatgtttaatcgtttctcacacttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73960.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA17G13080.1 (Glycine max), 3'ss of exon 14
gtgttgtgctcttacttctagacatctcaaaatcctacattggttacagt--tcatgtttaatcgtttctcac-acttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
|| | | | || | | | || | | | || | | | ||| | ||| | | || | | | || | || | || |||||||| ||||||||||| ||||||| |||||||||||||||||||||| | ||||| || | ||| | || ||||| ||||| ||||| |
---atgctcattcatttgtgatggtgtttgtattttgtacctttcactatcatagtcttttgtagttatttattgattctagacatttggcttcttcttttagATCAATCAATTAGAGAAGGACAAAGATGTTATTGCTCAGGCACAAGCAATTGCAGCCCTTGAGGCATCCCCACAGCTATCATTTTCTATTGTTAATGCCC
upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA05G07920.1 (Glycine max), 3'ss of exon 14
---gtgttgtgctcttacttctagacatctcaaaatcctacattggttacagttcatgtttaatcgtttctcacacttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
||| || | || || | | || ||| || | || | || | ||| || | || | | | | | | || || | || |||||||| ||||||||||| ||||||| |||||||||||||||||||||| | ||||| || | ||| | || ||||| ||||| ||||| |
catttgtgatgtttgtattta-gtatctttctctatcatagcctt-ttgtaattggttttttattgatttattgattc-tagatatttggtttcttcttttagATCAATCAATTAGAGAAGGACAAAGATGTTATTGCTCAGGCACAAGCAATTGCAGCCCTTGAGGCATCCCCACAGCTATCATTTTCTATTGTAAATGCCC
upper sequence: AT1G73960.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv17s0000g04200.t01 (Vitis vinifera), 3'ss of exon 14
---gtgttgtgctcttacttctagacatctcaaaatcctacattg-gttacagttcatgtttaatcgtttctcacacttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
| || || | || | ||| || |||| | | | || | || | ||| | | | | | || | | || ||||| | |||||| |||||| |||| ||||||||||||||||||||||||||||| |||| || || ||| || | || ||||| |||| ||||| |
attggattctgttgaatctattgttttatataaatcacttcattctatcaaatttgaaagtt--ttgttaatgatgttgataaaat--tggaattcttaatcagATTAATCAATTAGAGAGGGACAAGGATGTTGTTGCTCAGGCACAAGCAATTGCAACACTGGAGGCATTACCTCAGCTTTCATTTTCTGTTGTTAATGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagttcatgtttaatcgtttctcacacttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
ttctcac putative branch site (score: 2)
tttctgtcactttt putative PPT
atgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttgtgctcttacttctagacatctcaaaatcctacattggttacagttcatgtttaatcgtttctcacacttgtgggtttctgtcacttttgatcagGTCAATCAACTAGAGAAGGACGGAGATGTTGTTGCTCAGGCACAAGCAATTGCGTCACTTGAAGCCTTAAAACAACACTCCTTTTCCATTGTGAATGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC