Sequence
atgc intronic sequence ATGC exonic sequence...accacttaatgaagtgttatatgtagttatttttgcattagacaagtgagctcgttgagctcttttatggcttcttatacggactcctttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52660.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 2
accacttaatgaagtgttatatgtagttatttttgcattaga--caagtgagctcgttgagctcttttatggcttcttatacggactcctttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
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--gaattgttgagatttctactatttttccaatagcttcagtgcttaatggatatctcaaatacctataagaaggactgaaaaattactactgattttgtagATACGTAGCCATGCTCAGAAATACTTTCTAAAAGTTCAGAAGAGTGGGACAAATGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGCTCATCCAT
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 2
accacttaatgaagtgttata--tgtagttatttttgcattagacaagtgagctcgttgagctcttttatggcttcttatacggactcct-ttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
|||| | | ||| || | | |||| ||| || | | | || | | | | || || | | || | | || ||||||| || ||||| ||||| || ||||| || || || ||||||||||| |||||||||| || || || || |||||||| ||||| || |||||||
---ttttaaatctgcttaataattgaatgcctctttgaattcctcacccaaacacactgtaatttagtttaaggactaatgataatttctactgactttgtagATACGTAGCCATGCACAGAAATACTTTCTAAAAGTTCAGAAGAGTGGGACAAGTGAACATCTTCCACCACCCCGGCCTAAAAGAAAAGCTGCCCATCCAT
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G24400.1 (Glycine max), 3'ss of exon 2
accacttaatgaagtgttatatgtagt-tatttttgcattagacaagtgagctcgttgagctcttttatggcttcttatacggactcct-ttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
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--ttttaaatccacttaaaaattgaatgcctctttcaattcctcaccccaacacactgtaatctagtttaaggactaatgataatttctactcactttgtagATACGTAGTCATGCACAGAAATACTTTCTAAAAGTTCAGAAGAGTGGGACAAGTGAACATCTTCCACCACCCAGGCCTAAAAGAAAAGCTGCCCATCCAT
upper sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 2
----accacttaatgaagtgttatatgtagttatttttgcattagacaagtgagctcgttgagctcttttatggcttcttatacggactcctttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
| | || | ||| ||| | ||| || | | || || | | | | || || | | | | | | || | ||||||| || |||||||| || || ||||| || || || ||||||||||| |||||||||| ||||| || |||| ||||| ||||| | ||||||||
tctgagtatatatgggagttatatgaattgttgagatttcttctatttttcgatttc-tcaaatacctataaggactgaaaaattg---ctactgattttttagATACGTAGCCATGCTCAAAAATACTTTCTAAAAGTTCAGAAGAGTGGGACAAGTGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGTTCATCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagctcgttgagctcttttatggcttcttatacggactcctttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
ctttaat putative branch site (score: 4)
ctccttta CT-rich tract
tttaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accacttaatgaagtgttatatgtagttatttttgcattagacaagtgagctcgttgagctcttttatggcttcttatacggactcctttaatactgcagATACGAAGTCATGCTCAGAAGTATTTTCTTAAGGTACAAAAGAGTGGGACCGGTGAACATCTCCCTCCTCCTCGACCTAAAAGGAAAGCCGCTCATCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA