Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 2
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
|| ||| || || || | | | | || | | || | | || ||| ||||| ||| | | || ||| ||||| ||||| || ||||| ||||| || || ||||| || |||||||| |||||||| ||||||||||||||||||||||| |||||| |
gtgagttgtacattctaataatttctactagcatgatgctatcatctataacatcaacttctgagtt----gtgacttctattttc----tatgacagAATGGAGTCAATAAGCTTGCTGATCTCGTTGGAGTCACCCTTGGTCCAAAAGGACGGAATGTTGTCCTTGAGAGCAAGTATGGATCACCTAAAATTGTCA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
gtaagtatc---ttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgt-tgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
|| || | || || | | | | || || || | | | | || | || || | | || || | | | | || |||| || |||||||| || || |||||||| |||||||| ||||| || ||| | ||||||||| | |||||||||||||| || || | ||||| |
gtgagctccaaagttcttggacacatcttatcaaattttggtcacta---tgattcttagccttgac----caggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G015989_T02 (Zea mays), 3'ss of exon 2
gtaagtatcttttttaaaaaaagttaatg---ga--aacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaatt--ttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
|| ||| | | || | | ||| | || || | | || | | | || | | || | || || || || | | | || ||| ||||||||||| |||||||| || || ||||| |||||||| || || |||||||| || || || ||||||||||| ||||| |||||| |
gtgagttttctgacaaacatataataacgcttgactaaggccgccgctgctcctcacgttcaagtgtgcgttgcacttacttattacttgattttcctatgtcagAATGGGGTCAACAAGCTTGCAGATCTCGTCGGGGTTACTCTTGGACCAAAGGGGCGAAATGTAGTCCTCGAAAGCAAGTATGGCTCACCTAAAATTGTCA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
|| || | || | ||| | || || | || | | | | ||| ||||| | || || |||| ||||| ||||| ||||| || || || |||||||| ||||| || ||| | ||||||||| | |||||||||||||| || || ||||||||
gtgagctccacagtttttatttattatgatataccgatttgctg---ttgacccttaaccaggcgctaattgttttttctc-ccctacatt---tcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 1
gta-agtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
||| | ||| | | | | | ||| | |||| | | | || | | |||| || | ||| ||| | ||| | | || ||||| ||||||||||| ||||| ||||| || || ||||| ||||| ||| ||||||||||||| |||||||||||||| || || ||| ||||
gtataatataacactcctcgctcgctgtgactag--tgattgcgaaacgcgcgttttgagtgt-cgtttt-tgagtttt----tttcgcgttttgcagAGC-GGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGAAATGTTGTTCTCGAGAGCAAGTATGGCTCGCCGAAAATCGTTA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggttt----acattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
| || || | | | |||| | | || | | || | ||||||||| | | || ||||| ||||||||||| ||||| ||||| || || ||||| ||||| ||| | ||||||||||| || |||||||| || || || ||| ||||
--------------------------gtacgtgctgtatatc---gctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGC-GGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ16507 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtatcttttttaaaaaaagttaatggaaa---cttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
||| |||| ||| || | | || | || | | | | || |||| || | | ||||||| || ||||||||||| ||||||||||| || || | || ||||||||| | ||||| || || ||||| |||||||| || ||| ||| | |
----------------------gtttgcagaaaagctttctctctcggattggcattgggccattggcgagtttttcttatcgggtttt-tgc-gaaacagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGTAAGTATGGTTCTCCAAAGATTATCA
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtatcttttttaaaaaaagttaatggaaa---cttcattcccaaaccggagctaaag-gtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
||| |||| | | || | | || | || | || | || | ||| || | | ||||||| || ||||||||||| ||||||||||| || || | || ||||||||| | ||||| || || |||||||||||||| || ||| ||| | |
----------------------gtttgcagaaaagcttcctctctcggattggcattgggccattggcgagtttttc--ttatcgactttttgc-gaaacagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGCAAGTATGGTTCTCCAAAGATTATCAMapped 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|47830371|gb|CK120055.1|CK120055EST: AGGAGACTTCAA GCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAA
genomic: AGGAGACTTCAAgtaagtatct ... gttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
ttctaat putative branch site (score: 2)
tttctaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatcttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgttgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG