Sequence
atgc intronic sequence ATGC exonic sequencegtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 16
--------------------------------------gtacagatttacgcttttagtagtgaagatgagcatatgatattca-attgttgaac-atatactgcaagctttactactcctcactgtttgcac-caaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
| | | || | ||| || || |||| || | | || || || || || | | | | | || | | || ||| ||| ||| | |||| || || | | || | | ||||| ||||||||||||||| |||||||| ||||| || |||||||| ||||| ||||| || |||||||||
gtatgggctatgtcatactaaccttcctgcaataaaaaggaagcctcgacttcctgagtggttttga-aagcaattgctccccttgttatttaattatttatgtctaatgtcgagattat--gttgctaacctgcataatctgtcaaaaatagcatcatttatgaacaatttaatatttggtctctgttaacagATGTCTGCAGCCGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTAACACCAATCCTG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 18
--------------------------------------gtacagatttacgcttttagtagtgaagatgagcatatgatattca-attgt-tgaacatatactgcaagctttactactcctcactgtttgcaccaa-aatatgtgaaagagctcatcgc--atagaaaaatgtaaact-gatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
| | || || | ||| || || |||| || | | | || | | | || || | | || | | || | | | ||| ||| ||| | ||| || | || | || | | ||| || |||| ||||||||||||||| |||||||| ||||| || |||||||| ||||| ||||| || |||||||||
gtatgggctatgttacactaaccttcctgcaatcaaaaggaatccttgacttcctgagtggttttga-aagcagttgttctccttgttatctaattatttatgtctaatattgagattat--gttgctaacctggataatctgtcaaaaataatatcatttatgaagaattttatatttgatctg---tgttaacagATGTCTGCAGCTGCTTTTGCCAAAGGTCTTCTTGACCTTGAAGGGCAGCTCACACCAATCCTG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 20
-----gtacagatttacgcttttagtagtg--aagatgagcatatgatattca--attgttgaacatatact-gcaagctttactactcctcactgtttgcaccaaaatatgtgaaag-agctcatcgcatagaa--aaatgtaaactgatttg--------cactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
| | | || ||| || | |||| | | || | |||| |||| | | || | | ||| | | | ||| | | | | | | | | | || | | | | |||| | | ||| || | ||||||||||||||| |||||||| ||||| || ||||||||||| || ||||| || |||||||||
gtatggcctaaagttgtgctcaccttaatcataagaaggctaagtggttttcattattggttgctacatttttatacattttggaagtgtttgatgtctaggc-attgtttataagcctaatttgtcctttggcatcatatgtgagccattttttcatgacccatattaaacagATGTCTGCAGCTGCTTTTGCCAAAGGTCTTCTTGACCTAGAGGGGCAGCTAACTCCAATCCTG
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 16
----gtacagatttacgcttttagtagtgaagatgag--catatgatattca--attgttgaacatatact-gcaagctttactactcctcactgtttgcaccaaaatatgtgaaag---agctcatcgcatagaa--aaatgtaaactgatttg---------cactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
| | | || ||| || | || | || | || | |||| |||| | | || | | ||| | | | ||| | | | || | | ||| | | || | | | | |||| | | ||| || | ||||||||||||||| |||||||| ||||| || ||||||||||| || ||||| || || ||||||
gtatggcctaagttgtgctcaccttaataaaaaaaaggctaagtggttttcattattggttgctacatttttatacattttgtaagtgtttgatgtctaggc-agcatgtttataagcctaatttgtcctttggcatcatatgtgagccatttttttcatgacccatgctaaacagATGTCTGCAGCTGCTTTTGCCAAAGGTCTTCTTGACCTAGAGGGGCAGCTAACTCCGATCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
aactgat putative branch site (score: 3)
atagaaaaatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagatttacgcttttagtagtgaagatgagcatatgatattcaattgttgaacatatactgcaagctttactactcctcactgtttgcaccaaaatatgtgaaagagctcatcgcatagaaaaatgtaaactgatttgcactgttgacagATGTCTGCAGCGGCTTTTGCTAAAGGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA