Sequence
atgc intronic sequence ATGC exonic sequencegcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
-----------------gcaagtcaaccatcaca--tcattctaatgtag-aagttgtattgaaaaatcatgcatgaat--gtgaaaaactttaacacttcattatctttttaaatctatcagac--atatataatagcaacccct-caccttct-ttgccaccataattct---------cttgttc-agGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
|| | | |||| | || |||| || | || | |||| ||| ||| |||| ||| ||||||||| | || | | | | | ||| || | | ||| | ||| | | |||| |||| || |||| ||||||||||| |||||||||||||| || ||||||||| || ||||| || |||| ||| || ||| | ||||||||||| ||||| || || |
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 5
------------------gcaagtcaaccatcaca--tcattctaatg--tagaagttgtattgaaaaatcatgcatgaa---tgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgc-cacca-taattctc--------------ttgttc-agGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
|| | | |||| | || |||| | ||||| || | |||| ||| || || || ||| ||||||| | || | ||| | | | || ||| | | ||| | ||||| || |||||| |||| ||||||||||| |||||||||||||| || ||||||||| || ||||| || |||| ||| || ||| | ||||||||||| ||||| || || |
gtaactgggtttttccttttaacttttcaatcaaggttaatgggaatgagtcaaagtt-tacaggcaaatgcggcaaaaaatagactaataaatttgttgcttcattcttgccttttgt-tattgaatctgaaaaagggcagtgatttgtgtctattgtatgctgctaattttcatctaacaagaagcttgttccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctc-ttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
||| || | | ||| || | ||| || || |||| ||||| | ||| |||| || | | | | || | || ||||| |||||||||| || || ||||||||||||||||| |||||||| ||| ||||| ||||||| |||||| ||| ||||||| || || ||||| || || |
------------------------------------------------cattcaggttccatagaaatttgggctagacataatgga--tagcactat--gacatttcctgtagt----cctctgattatgttctaacaagctgcttgttgtttagGTGAGTCACCACCCAATGATTGTTGCTTGCCACTGTGAGGGGAGAGGCTGGAAGTTCTGGGCAGACTCTAATCTCAAAGGGAAGTTCTGGGGCCGTTCCA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaaca-cttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
| | | || | ||| ||| | || | ||| | || | | || || | | || | | | | | || || | ||| | ||||||||||||||||| |||||||| || || ||||| ||||| ||| ||||| |||||||| ||| ||| | ||| | || |||||||| || ||||
-------------------------------------------------------ggagatattaatttgcaacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctt-tgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA
upper sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
| || | ||||| | || || || | ||| || | ||| | || | || | | ||| || || | |||| ||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| |||||||| ||| || | ||| | || |||||||| || || |
---------------------------------------------------ctttaaacatttcgaacttcagaac---ataatatgagctaattaatttg-catcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
ccctcac putative branch site (score: 3)
ttctcttgttc putative PPT
atataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA