Sequence
atgc intronic sequence ATGC exonic sequencegtaacccaccccgaccagtcattttatatgttccaagtgatgaaacaaggttttttgtgatattattgatctctgctttcctggcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G47850.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G17260.1 (Glycine max), 3'ss of exon 3
----------gtaacccaccccgaccagtcattttatatg--ttccaagtgatg-------aaacaaggttttttgtgatattattgat-ctctgctttcctg----gcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
| ||| | | | | ||||| ||| || || | | || || ||||| || || | || ||| ||||| ||| || ||||||||||| ||||||||||| || || || ||||||||||||||||| |||| |||||||| | ||||| | |||||||||| | |
gtatagtttttttccccctttaaatgatttgctctatataaattctaaaaaatttcttcttacatttccaattcaatgtggttattaatacttggtgtttctgatgagcagTATTATTTAAAAACTGGAACCTGTAAATTTGGTGCATCCTGTAAATTCCACCATCCAAAAAATGGAGGTGGATATTTAAGCCAAGCTCCACTAAATGTTT
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 3
-----------gtaacccaccccgaccagtcattttatatgttccaagtgatgaaaca---aggttt----tttg---tgatattattgatctctgct-ttcctg----gcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
| | | || | | ||||| | || || | || | | |||| ||| || | || | || || | || ||| ||||| ||| || || |||||||| ||||||||||| || || || ||||||||||||||||| |||| |||||||| | | ||| | |||| ||||||| |
gtatagtttttttttttctctcccttaaattatttttttcattgtaaatctggagattgttatgtttccaatttaaaatggttatactaattcttgttctttctgatgagcagTATTATTTAAAGACTGGAACCTGTAAATTTGGTGCATCCTGTAAATTCCACCATCCAAAAAATGGAGGTGGATATTTAACCCAAGCTCCATTAAATATTT
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 3
------------gtaacccaccccgaccagtcattttatatgttccaagtgatgaaacaaggttttttgtgatat----------tattgatctctgct-ttcctg----gcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
| | | | ||||| | | || | |||| | ||| ||| | || | || || | || ||| ||||| ||| || || || ||||| ||||||||||| || || || ||||||||||||||||| |||| |||||||| | ||||| | |||||||||||| |
gtatagtttttttttttttttttccttaaatgattttttcaatgtaaaatctggaaattgctatctttccgatttaaaatggttatactaattcttgttctttctgatgagcagTATTATTTAAAGACCGGAACCTGTAAATTTGGTGCATCTTGTAAATTCCACCATCCAAAAAATGGAGGTGGATATTTAAGCCAAGCTCCACTAAATATTT
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G02540.1 (Glycine max), 3'ss of exon 3
-----gtaacccaccccgaccag-tcattttatatgttccaagtgatgaaaca----aggttt-----tttgtgatattattgat-ctctgctttcctg----gcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
| | ||||| | | |||| | | || | ||||| | ||| || || ||||| | || | || || ||||| ||| || ||||||||||| ||||||||||| || || || |||||||||||||| || |||| ||||| || | ||||| | |||||||||| | |
gtataattattttccccgtttaaatgatttgctcaatgtaaaatctagaaacttcttatatttccaatttaatgtggttattaacacttggtgtttatgatgagcagTATTATTTAAAAACTGGAACCTGTAAATTTGGTGCATCCTGTAAATTCCACCATCCTAAAAATGGAGGTGAATATTTAAGCCAAGCTCCACTAAATGTTT
upper sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------------------gtaacccaccccgaccagtcattttatatgttccaagtga----tgaaacaaggttttttgtgatattattgatctctgctttcctggcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
|| | | | | | |||| || | | | | | | || | || ||| | | | | ||||||||| ||||| ||||| || ||||||||||| ||||| |||| || |||||||||| |||| ||||||||||||||||| || |||||||||| |
gtatgttgttgtttgttgactgaatataaaatactggatggggatggaatgcttgatctctaccaatatagattccttggatctgctagaattgttttcatctacttgtattatgcattattattaaggcttattatcctatacttattaatcgtatagttattccttaaatatgcagTTTTATTTGAAGACTGGGACCTGTAAATTTGGTGCGTCCTGCAGGTTTCACCATCCAAGAAATGGTGGTGGATCCATGAGCCATGTGTCACTAAATATTTMapped 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|164056652|gb|ES079706.1|ES079706EST: TTAGAGCTACCGGGCAGTATCCTGAACGTTTTGGTGAACCCCCATGCCAG TTTTACTTGAAAACTGGAACTTAGTAAATTTGGGGCGTCA
genomic: TTAGAGCTACCGGGCAGTATCCTGAACGTTTTGGTGAACCCCCATGCCAGgtaacccacc ... ttcctggcagTTTTACTTGAAAACTGGAACTT-GTAAATTTGGGGCGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaagtgatgaaacaaggttttttgtgatattattgatctctgctttcctggcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
tattgat putative branch site (score: 3)
tctctgctttcct CT-rich tract
ttttttgtgatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacccaccccgaccagtcattttatatgttccaagtgatgaaacaaggttttttgtgatattattgatctctgctttcctggcagTTTTACTTGAAAACTGGAACTTGTAAATTTGGGGCGTCATGCAAATTCCACCATCCAAAGAATGCAGGTGGATCCATGAGCCACGTTCCACTAAATATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA