Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G64390.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g12030.1 (Oryza sativa), 3'ss of exon 1
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcataca-gtacta-actagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
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--------------------------------------------------------------------------gtacgtgc-tcccgccattgtggcagctagcaaacctgcaatct-ttctctgctcttg----atcttgatcagtacggtttaatttgcaagaacgtgttctattctacacatctacatt--tcagGTGGATCTTGTTGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCCTCGAGT
upper sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g12070.1 (Oryza sativa), 3'ss of exon 1
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcatacag-tactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
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-----------------------------------------------------------------------------------------------gtacgtggagtcgttcaccattt--tctccgttcttgaa---ttgcaggatgtgttctaca-gctccatgcatctgatctgttgattttttttcttttttcagGTGGATCTTGTTGGTGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGGCTGCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCATCGAGT
upper sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgt-tgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgt--tcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
|| ||| | || | | | | | | || || | || | | | | ||| || | | ||| |||||| | | | | || | | | || || || | | | | || | ||| |||||| |||| || |||||||| || || || || |||||||| || ||||| || || ||||| ||||||||||| |||||| ||||||| | | ||||
---------------------------------------------------gtatgcaccattctaccttcaaatct---ttgatcaaaaccatgatgccatcaat-ggcattgtgttcaattt--gttcaggagatatgatgagttgggttctaatggagtgcaatgca--aatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT
upper sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatag-atctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
| | | || | | | | ||| | | || || | | | || | | ||| ||| || || |||| || ||||| || || || | | | | | |||||| | || |||||||| ||||||||||| || ||||| ||||| || || | || ||||| ||||||||||| |||||| ||||| | | | ||||
---------------------------------------------------------gtatgcacaacgcgtctctcgttgcatt-aattagcaagcaagcattgtgaccatggcagctgggttc---------gtcgctgtgctgaacacgatttttgttttg----gttctt-ttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accaacattgttcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
tactaac putative branch site (score: 0)
tcttttgt putative PPT
aatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatagatctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG