Sequence
atgc intronic sequence ATGC exonic sequencegtaacaagaaaccgtagagttatttcccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24940.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S174_123V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------gtaacaagaaaccgtagagttatttcccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG
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gctccttcctcttgtagtatgctgttctcatttttgggctgtgtggtccactgctccaattgaagaaatattggcttaagcacggtattcgt---ttgtccagGCACTTGGCGTGTAGGTGGCGTTCTTGCAGTCTCTCGGGCGTTTGGTGACCGATTGCTCAAAAAGTATGTTGTTGCGGAACCAGAAATTCAG
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
-------------------------gtaacaagaaaccgtagagttatttc-----ccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG
| | | | | ||||||| | |||| || | | || ||| | || |||| |||| |||||| | || || || |||||||| || || || || ||||||||||| |||| ||| ||||||||||||| || ||||||||||||
aaagtatcattctctatcgttttattttattttattttatttatttatttcatctatctgtttgaggagcactgtctta-gtgataagttc---gattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttcccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG
gcctaac putative branch site (score: 2)
ttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaagaaaccgtagagttatttcccgctttgtggcttattttccggtgtgcctaactcctagattgaacagGGACTTGGAGAGTTGGAGGAGTTCTTGCAGTTTCCCGCGCGTTTGGTGATCGATTGCTTAAACAATATGTTGTTGCTGATCCAGAAATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT