Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G19960.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
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------------------------------------------gtaaggataaatctgaacttcttttctcctttatttgggagtt--ctatggcttttatagtgatactatattgtactg-tagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 3
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgc--tagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
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-----------------------------------------------------gtaagaagtgatgtaaactttttttttgagttcaat--taatggctttattattgatatttatcgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCTGTCAATCCTTTCAAGAAAGTTTCACTGTATGGTAACGAGTACATCGATGCATATAGAAATAAATCAATGGATA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 3
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgc--tagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
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------------------------------------------gtaagaagtgatgtgaactttttattttttatg-----gaattcaat--taatggctttattattgatatttatcgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCTGTCAATCCTTTCAAGAAAGTTTCTCTGTATGGTAACGAGTACATTGATGCATATAGAAATAAATCAATGGATA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 2
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatat-atgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
|| | ||| || | | | ||| |||| | | ||| ||| || || || | || || | || | |||| | | | || |||||||||||||||| |||||||| ||| | ||||| |||||| | |||||| |||| || ||| || |||||||| |||| | ||| ||| ||| |
-----------------gtaagtctttatgtctct-----ttaaagtttttctcatcaattagtttcttgatcataactttgaatgtatttatgtgta--taactatgtacaatt-------cagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA
upper sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 4
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatat-atgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
|| | ||| || | ||| | | |||| | | ||| |||| || || || || || | || | |||| | | | || |||||||||||||||| |||||||| ||| | ||||| |||||| | |||||| |||| || ||| || |||||||| |||| | ||| ||| ||| |
-----------------gtaagtctttatgtctctt----taaaaat-tttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgta--taactatgtacaatt-------cagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
ggctaac putative branch site (score: 2)
cctttttcctttat CT-rich tract
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA