Sequence
atgc intronic sequence ATGC exonic sequence...tccttgcatactttcttgagcatattatgttttcattgttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G71310.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
------tccttgcatacttt-cttgagcatattatgttttcattgttttgcttg--taacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
| || || ||| | |||| || || ||| ||| || || |||| | | | ||| | | | | || || ||| | | |||| | || ||| | || || || | |||| ||||| | ||||||||| ||| ||||||| ||||| ||||||||||| |||||||| || ||| |
tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatg-gtagaactgacctatttgggat-atatttct-------ttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
upper sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
tccttgcatactt-tcttgagcatattatgttttcattg--ttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
|| || | ||| || | | ||||| | || || | | ||| | | | | | || || ||||||||||||||||||| ||||| | || ||||| |||| | | ||||| ||| |||| || ||||| ||||||||||| ||||| | || ||||||
-gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtcttattgacc--cggtaagtcccatttatttctctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC
upper sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
tccttgcatactttcttgagcatattatgttttcattg---ttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
| | |||||| || || | | | | | | | | | | || | | | |||| ||| |||| ||| | | | |||| | || || |||||||| || | | ||||| |||| ||||||||| ||| |||| || ||||||||||||||||| || | ||||| ||||||
-catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaag-gaaaactaacttgaattgcccgtaa-cattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
tgctaat putative branch site (score: 2)
aaatcatttgctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccttgcatactttcttgagcatattatgttttcattgttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
