Sequence
atgc intronic sequence ATGC exonic sequencegttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50950.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------------gttcggaatcagatcttta--cgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
||||| | | | | | | || | |||| | | ||| | ||| | | | | ||| | |||| || | ||||| || ||||||||||| ||||| ||||||||||| || || || || |||||||| ||||| | || ||| |||| || ||||| || |
gtgcgtgtggtttcggtttctctctcctcccgcatggattgctaggaggtgtttcgatctgttcgtgacggatgccgtggttggttttgattgatctgttgatggggggtgcttttcgtggttgtatgtatgt-atcctgt---agGCTGTGGGGCGCGCAGACGCAGAGGTCGCTGCAGAACTTCGACATCGGCGGCGAGCGCGAGCGGATGCCGGTGCCCATCATCCGCGCCTTTGGGGTGCTC
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 1
gttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
||| | |||| | | | || | || || | | ||| | | ||| | | |||| ||||||||||||||||| || || |||||| | ||||||||||| || ||||| |||||| || ||||||||||| ||| | || |||||||| ||||||
gtttgttccttctcctttcccactcttttcttgactatttcttagtatctgattgtgttgtgtttctgcacta--ctgttatagATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGACATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCTTTTGGCGTCTTG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 1
-----------gttcggaatcagatctttacgatat-atatcgttctgatctcgagggaaaatattctcacatttttatttgttgtt------ctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
| | ||| | | | || || | | | | | | || || ||| | | |||| | |||| ||||||||||||||||| || || |||||| | ||||||||||| || ||||| |||||| || ||||||||||| ||| | || || ||||| ||||||
gttcgttcgtcttccttaattaatttccctttctgccatttcctctttttttttttttcatttcttatctgattgtgttgtgtttctgaactactgttatagATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 1
-----------------gttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttt-tatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
| || | | | | | | || | | | | || | | || | | | || | |||| ||||||||||||||||| || || |||||| | ||||||||||| || ||||| |||||| || ||||||||||| ||| | || || ||||| ||||||
gttcgttcgtcttccttaattaatttcgctttctgccatttcctctttttttttttttcacttcttatctgattgtgttgtgtttctgaactactgttatagATTATGGGGAGCACAAACTCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
| | | | | |||| | || | | | | | | | || |||| | | |||||| | || | | | ||||||| ||||| ||||| || || ||||| | ||||| || || ||||||||||| || || | |||||| ||||||||| | ||||||||||| || |
acggatgtatagaagtgatgtgatacaaaagatttaagttaattctggaataggtatggtaataacttattttta-atttttttggactgatatctttcagATTGTGGGGTGCACAAACTCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
ttctcac putative branch site (score: 2)
ttgttct putative PPT
aaaatattctcacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggaatcagatctttacgatatatatcgttctgatctcgagggaaaatattctcacatttttatttgttgttctgtgtcagATTATGGGGAGCACAGACGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT