Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatcaggaacccgtcctaatacttcaattatattttcgaaccctgataaaatgtgaaactactgatcattttcatttgcaaatggtgcttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35920.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 14
gtaagcatcaggaacccgtcctaatac--ttcaattatattttcgaaccc-tgataaaatgtgaaactactgatcattttcatttgcaaatggtgct-tttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
|| ||| | || || || ||| |||| | | | | | || | | | | | ||| | ||| | ||||||||||| || | ||| | | ||| |||||||| || |||| || |||||||| ||||| ||||||||||| || || ||||||||| |||| ||| | |
----atctcttttccccatttcaacacacttgaatcatatctactttcgtgttccagaacataagtttgcagtatgggttcttacttccatgatataatttcagGCATATAATTATTATGGAAAGGATCTGGAGATGGTATGTGCTGTCCTATGTGCTGGGCTTTACCCAAATGTCGTTCAGTGCAAAAGACGAGGCAAGAGGA
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 16
----gtaagcatcaggaacccgtcctaatacttcaattatattttcgaaccctgataaaatgtgaaactactgatcattttcatttgcaaatggtgcttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
| || | | | || | | ||| || || | |||| | | | | | | || || | || |||||||| |||| ||| | | ||| |||||||| | | || || | || || |||||||||||||||||||| ||||||||||| |||| ||| | |
aactaaatctattaagtatttgtgaattttggtgggacataattctctacagtttctaaat---agttcagggtggctccttacttccatgctataactt-cagGCATATAACCGCTATGGTAATGATCTGGAGATGGTTTGCGCTGTCTTGTGCGCTGGGCTGTACCCAAATGTTGTGCAATGCAAAAGGCGAGGCAAGAGGA
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 17
----------------------------------------------------------------gtaagcatcaggaacccgtcctaatactt-caattatattttcgaaccctgataaaatgtgaaactactg--atcattttcatttgcaaatggtg-cttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
| || || | | | || ||| |||| || | | | | |||| | || | | || | || |||| |||| |||||||| ||||| | ||| |||||||| | |||| |||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || |
gtaagcccctaatcccagttgcttttcttttcaactgaaatactttcccccatcttcccgcccatttagtttccatctcttcttaaagtaaaagcaagtatagcttatggctatattctgaataagtactaggagagtagttatgaagcataatttatgtctttgcagGTTTACAACCAGTATAGTCATGATTTGGAGATGGTTTGTGCAATTCTTTGTGCTGGGCTCTACCCTAATGTTGTTCAGTGCAAAAGAAGAGGAAAACGGA
upper sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 14
gtaagcatcaggaacccgtcctaatacttc---aattatattttcgaaccctgataaaatgtgaaactac-tgatcattttc----atttgcaaa-tggtgc-----ttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
| || |||||| | | | |||| || || | | | || | ||| | || | ||||| ||| | | | | | || ||||| || || ||||||||| | ||| |||||||| || |||| | || ||||| ||||| |||||||||||| | || |||||||||||||| ||||| |
--------------tctgtactaatattccctgagttattgcctctaaactgatttatatctaaaaaaaggtggtttttttccaggattagtagactaatatatgtgcttgcagGCCTATAATCAATATAGCAATGATCTGGAGATGGTATGTGCAATCCTTTGTGCTGGGCTCTACCCAAATGTTTTGCAGTGCAAAAGAAGAGGAAAGCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgataaaatgtgaaactactgatcattttcatttgcaaatggtgcttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
tactgat putative branch site (score: 2)
tgcttttc putative PPT
attttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatcaggaacccgtcctaatacttcaattatattttcgaaccctgataaaatgtgaaactactgatcattttcatttgcaaatggtgcttttcagGCATACAACCAATATAGCTACGATATGGAGATGATAAGTGCGGTTCTATGTGCGGGGCTGTACCCAAATGTTGTCCAATGCAAAAGAAGAGGGAAGCGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG