Sequence
atgc intronic sequence ATGC exonic sequenceGTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49460.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgag---aggaactaactat------gtgaaaattttgttttaacttgttttctgttatacag
| ||||| ||||||||||||||||| || |||||||||||||| || ||||| || || || || || || || ||||| || || || |||||| | ||| ||| | | |||| | ||||| || | | ||| | | | || || | ||| ||| ||| ||| || | |||
GAGAAACACCTTCTGTTGCTGGAATAATCAATCCTGGTTCTGATGGGTTTCAGAAACTTTTCTTTGGACAAGAAGAAATTGCCATTCCAGTTCATCCTACgtgagtgctctgctcctcatataagttcatgtgtacattaacagattgttcgtttgtaaacaatttatttatactcatttatatttttgcag
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G033226_T01 (Zea mays), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttg-agaatgtcatgtgagtt-cttga--gaggaactaactatgtgaaaattttgttttaact-tgttttctgttatacag----------------------------------
| ||||| ||||||||||||||||| || |||||||||||||| |||||||| || || || || || || |||||||| ||||| || |||||| || |||||||| || || || | | | |||| | | || || | | | ||| || | ||| || | |||| | ||
GAGAAACACCTTCTGTTGCTGGAATAATCAATCCTGGTTCTGATGGTTTTCAGAAACTTTTCTTTGGACAAGAGGAAATTGCTATTCCGGTTCATCCCACgtaagttctgtaggtcttcgtatctgccatttgattgggcaagaaaattgttctagctttggtgatgactatgctatctgattgctagcacagcttggtatttacttgtgtattttttgtag
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G36840.1 (Glycine max), 5'ss of exon 4
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatg-tgaaaattttgttttaacttgttttctgttatacag--------------------
| ||||| || |||||||||||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||| || ||||| |||||||| | ||| || | || |||| | ||| | | | || | |||||| ||| | || ||
GAGAAACACCGTCTGTTGCTGGAATAATTAATCCTGGTTCTGAGGGATTTCAAAAGCTCTTTTTTGGTCAGGTGGAAATTGCCATCCCAGTTCATGCTGAgtacgtgtgtttgat-tcat---aattcacaaattgtctcttttctgctttaaatttgaacttagtgatccaaacataatcaagagtccccccccccccactcc
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G03700.1 (Glycine max), 5'ss of exon 2
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagt--------tttgagaatgtcatgtgagttct--tgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacag----------------
| ||||| || || ||||||||||| || |||||||||||||| || ||||||||||||||||| || |||| |||||| || || || |||||||| | ||| || || ||| | | || | || | ||| ||||| | | | | | ||||| |||| | | ||
GAGAAACACCGTCAGTTGCTGGAATAATTAATCCTGGTTCTGAGGGATTTCAAAAGCTCTTTTTTGGTCAGGTGGAAATTGCCATTCCAGTTCATGCTGGgtacgtgtgtttggttctggaagatgaagtaacttgtaatgaaaggaaattcttgttttgttgtccaagtttaatgtgttcttagccgtatgttgaattcttttttcag
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G15020.1 (Glycine max), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttata--cag----------------
| ||||| || || ||||||||||| || || ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| ||||||||| |||| || ||| || |||| | | || | | ||| | || ||||| | || ||| || ||| || ||
GGGAAACACCATCAGTTGCTGGAATAATTAACCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTTCATGCCACgtatgtgttgctcat-tcatttctatactaaaaatttcctatttttgcttgaatttgggatttggttggttgtagttgtagccaaggggagatttttcttt
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G04000.1 (Glycine max), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttata--cag--------------------------------------------------------------------------------------------------------------------
| ||||| || || ||||||||||| || || ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| || ||||| |||| || ||| || |||| | || || | | || | || ||||| | || ||| || ||| | ||
GGGAAACACCATCAGTTGCTGGAATAATTAACCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTGCATGCTACgtatgtgttgctcat-tcatttctgtactcaaaatttcctttttctgcttcaatttggaatttggttgcttgaagttgaagccaaggggagatttttctttattttagtggtcttcttactttttcagaatacaaagtaaccaactttagtgcttgacgttcttgtttgtctggggtgatttctgttgacttattttgcag
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G15010.1 (Glycine max), 5'ss of exon 2
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgtttt--ctgttatacag-----------------
| ||||| || || ||| ||||||| || | ||||||||||| || |||||||| || ||||| || ||||||||||| || ||||| |||||||| |||| || || || |||| | || || | | |||| || || ||| | ||| | ||| ||
GGGAAACACCATCAGTTTCTGGAATAATTAGCCCTGGTTCTGAGGGATTTCAAAAACTTTTTTTTGGTCAGGAGGAAATTGCCATCCCAGTTCATGCTACgtatgtgctgctcat-tcattactatactcgatttcctttttttgcttgaat-ttatgatttggttggttgtagttgtagccaaggggagatttttctttat
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S46_63V6.3 (Physcomitrella patens), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatg--tgaaaattttgttttaacttgttttctgttatacag----------------
| || ||||| ||||| ||||| | || || || || ||||| |||||||| ||||||||||||||||| ||||| |||||| | ||||| |||| | || | | | | | || | | || | || | || || ||| || | || || ||| |
GGGAGACGCCATCTGTGGCTGGTGTGATCAACCCAGGATCTGATGGTTTTCAGAAGCTCTTTTTCGGGCAAGAGGAGATCGCTGTACCTGTCCATGGCAGgtgtgagctaa-accttggaaagactcgtcaagtttgctctagtacaactcaagtgcttttttgaattagtgctcaagtattcgcttacaatacctttaat
upper sequence: AT5G49460.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S35_384V6.2 (Physcomitrella patens), 5'ss of exon 3
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgaga-ggaactaactatgtgaaaattttgttttaacttgtttt-ctgttatacag---------------
| || || |||||||| ||||| | || || || || ||||| ||||| |||||||||||||| ||||| |||||||| || |||| || |||| | || || | | | ||| | ||| | | | | || ||| | | || | || |
GAGAGACTCCTTCTGTGGCTGGTGTAATCAACCCAGGATCTGATGGTTTCCAAAAGCTCTTTTTTGGGCAAGAGGAAATTGCAGTCCCCGTGCATGGCAGgtgggtacaacatccggtgaacattgacctaagacagctctagcaagttcgcatttgtgtactgtagtacttagccaccatttggtccagctagtgctttMapped 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|125097850|gb|EL154176.1|EL154176EST: CTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGC CATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCA
genomic: CTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttg ... tgttatacagCATTGAGGCAGCTTGTGCTGCGCATCCAACAGCGGATGTATTCATCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAAACGCCTTCTGTTGCTGGAATCATAAATCCTGGTTCTGAAGGTTTTCAAAAGCTCTTTTTCGGGCAGGAGGAAATCGCTATCCCTGTTCATGCCGCgtaagttttgagaatgtcatgtgagttcttgagaggaactaactatgtgaaaattttgttttaacttgttttctgttatacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA