Sequence
atgc intronic sequence ATGC exonic sequencegtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25490.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttc---aatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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-------------------------------------------------------------------------------tttaat--gctacaactaatgctgtggcagcattgt-ttaacctttttt--tctttcaaaattt-ccaagaaactatgcctgtttatgtgtttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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--------------------------------------------------------------------------ataaaagatagtacacaaaatctattttctaggctaattgtgatagc----agtagttttttggtgtaaatgtgaatctcagttctacctta----tcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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---------------------------------------------------------------taaaagata--atcaacaaaatc---tattttctaggctat--tgttatagtagtagttttatttggtgtaaatgtgcatctcag-----ttctaccttatc-------ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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---------------------------------------------------------------------------------caattgatctcacaattcaa-atttattgggagtgcatttttctgttaagatcatgtttcttgaattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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------------------------------------------------------------gttttataattttta------aaattttccatgacca-----actgagtatatatgcta--tccaatgag------agac---aacgtgtaattccgtgttgctttggttttatctatgcagGAAGCTACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 6
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaat-acagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
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--------------------------------------------------------------------------------------------------------------------------------------gtaggcaattcgtgctctttcgtcctgtgctgattagtttggtttgcagGACGCGACAATCGAACAGCTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAGTCAMapped 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|124710952|gb|EH802354.1|EH802354EST: AATGGGGATGGCTCCTATCCTTGGGAAG GACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGAT
genomic: AATGGGGATGGCTCCTATCCTTGGGAAGgtatgaactg ... ttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGAT
EST:
gi|47830292|gb|CK119976.1|CK119976EST: GCTCTGCTCTAGCTTCAGTAATAATGGGGATGGCTCCTATCCTTGGGAAG GACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGAT
genomic: GCTCTGCTCTAGCTTCAGTAATAATGGGGATGGCTCCTATCCTTGGGAAGgtatgaactg ... ttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
tactaaa putative branch site (score: 1)
tctttc CT-rich tract
ttatcaaaaaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA