Sequence
atgc intronic sequence ATGC exonic sequencegtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
----------gtattgtctctt-aacttataacccaagtaagccttctttaatctctctctctctcttggtctgttaacgagaga-gcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
|| | ||| || | || | ||| | | | | | | |||| | | || | ||||| ||||||||||| ||||||||||||||||||||||| || ||||| || || || || || |||
attgttctgtttaacgattctagaagctttatctacagtcggttcctgacagtgcatgcaacctacatggttaatggcttccatttatatcacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
---------gtattgtctcttaacttataacccaagt-aagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
|| || | | || | | | || | |||| | | | | | || | |||| || | | | | || |||| ||||||||||||||||| ||||||||||| ||||| || ||||| ||||| || | ||||||
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgt-agGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 3
-----------gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggt--cagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
|| | | | | | | | ||| | | | |||| || | | | || || | ||||| ||||||||||||||||| || |||||||||||||| || ||||| |||||||| | ||||||
gtacgcatcatgtgtcttgttgttcatcctggctatagtgaaagtagagagggagacattagtctcagacctccagaagccaacaccttccatgcttgcagGTTGTTGAGATCACAAAGGGCAGTAAAGTGAAATATGAGCTAGACAAGAAGACCGGAATGATCAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
------------------gtattgtctcttaacttataac-ccaagtaagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
| || | || | |||| | || || || | | || | | | ||| | | ||| | ||||| |||||||||||||||||||||||||| |||||||| || ||||| || || || || || |||
atttgcttgtcgagcaaaaaagtgcattttttatcataatgtttaacaaatctact--agttcgcttcatacagtgactgcattatttaca-----tctttatgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-----------gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtc-tgttaacgagaga-gcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
|| | | || | || || | | | | ||| | ||| || || | | | | | |||||| |||||||||||||||||||||||||| ||||| || || ||||| || || || || || |||
ttgttgaggaaaaataagtgcatggtttttt-tttaattacgatatttaacaaatctagttagctccaaacaatgaccgcgttatataattttttattcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G05390.2 (Glycine max), 3'ss of exon 3
----------gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtc--tgttaacgagag-agcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
| |||| || | | | ||| | ||| || | | | | | |||| || || | || | || || | ||||| || |||||||| ||||||||||| || ||||| ||||| ||||||||||| || | || |||
tattcatgcaaaactgtcactccattcttgaccagaaatttcctactatg-tatgttatttatgcttgttcaatgcttacttgctcagttgctatttgcagGTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
----------gtattgtctcttaacttataacc--caagtaagccttctttaatctctctctctctcttggtctg-ttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG----------------------------------
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atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaat-ttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|19878118|gb|AU238949.1|AU238949EST: CATGGCACGACCTTGAGATTGGTCCTGAAGCTCCATTGGTCTTCAATGTG GTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAG
genomic: CATGGCACGACCTTGAGATTGGTCCTGAAGCTCCATTGGTCTTCAATGTGgtattgtctc ... ctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAG
EST:
gi|86073611|gb|DR369368.1|DR369368EST: CATGGCACGACCTTGAGATTGGTCCTGAAGCTCCATTGGTCTTCAATGTG GTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAG
genomic: CATGGCACGACCTTGAGATTGGTCCTGAAGCTCCATTGGTCTTCAATGTGgtattgtctc ... ctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
tgttaac putative branch site (score: 2)
cctctct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtctcttaacttataacccaagtaagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG