Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23310.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
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--------------------------------------------------gtcagtaatcatttttttac-cacttgatg--actcgatctc-ttgatatgcaaatctttttgacaagt---gatcattctg------gctgc-----gcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 6
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
|| | | | ||| || |||| | || || | | || | || | | | | | |||| |||| | | | || || ||| | ||||||| ||||||||||||||||| ||||| |||||||||||||||||| | ||||||||||||||||| |||||||||||||
--------------------------------ttttgcct--cagttttgacaagttttctttccccttctcgccatacgataactatatagattgatg---gcattttaagctt--------ttctttctttgcaat-------aatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
|| | | | ||| || |||| | || || | | || | | | | |||| |||| | | | || || ||| | ||||||| ||||||||||||||||| ||||| |||||||||||||||||| | ||||||||||||||||| |||||||||||||
--------------------------------ttttgcct--cagttttgacaagttttctttccccctgtggctgtacgatgactatatagattgatg---gcattttaagctt--------ttctttctttgcaat-------aatgcagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
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---------------------------------------------atttggtaacctcttgtt-ctgactttgttttggcaagttgctgacccctgttttgacaaactacga--catttgaagcttttct--ttcttttcaat--actgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgtt--caaa-tacagcttattaagtgaaatgc--tatcaat--tgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
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----------------------------------------------------------acatttggtaacctcttgtctg-actttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccgcagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
|| ||| | ||| | | ||||| | | | | ||||| || |||| || | || | || ||| | ||||||| |||||||| ||||| || |||||||| |||||||||||||| || | |||||||||||||| ||||| ||||||||
-----------------------------------------tcactttgttt---cctctgttataagaaatgt-ttatgcaggaccctgcgctaactgcataagggtttatatcaactaaacttttgatattggaat-------actgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG
upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatc-atcattactttattcatcttatggaagtttttctcactgata--tataagt------tttctgttcaaatacag-cttattaagtgaaatgc--tatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
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--gtaatcttctttgcattcc-attttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTGMapped 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|125027493|gb|EL099762.1|EL099762EST: TTACAAAACTGGCAGAGAAATAGAAGGATGCTT GCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAAGAAGTTTTGTT
genomic: TTACAAAACTGGCAGAGAAATAGAAGGATGCTTgtgagtttat ... tcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCA-GAAGTTTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
ttattaagtgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttatcgttcttttcttgttctgagatttctacttgccagattgaacaaatcatcattactttattcatcttatggaagtttttctcactgatatataagttttctgttcaaatacagcttattaagtgaaatgctatcaattgcagGCTTATTCTACAGTTGGAACTCCTGACTATATTGCTCCAGAAGTTTTGTTGAAGAAAGGATATGGCATGGAATGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA