Sequence
atgc intronic sequence ATGC exonic sequencegtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04850.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G092468_T02 (Zea mays), 3'ss of exon 2
---------------gtcagtgttttctttctg--cttc--ttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
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acaggagctctcccaaacgggacctaatagagaaccttcagtccgtccgttcgtcaacggttactaagctcctaatcttcaccctctgt-tttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT
upper sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 2
------------------gtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
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gaaataatttataacttcattcatatttcatgtaatagtacacatgaaatgaatattatatagctgtattcatatagcaatgcactatgcctttggttagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACGTTCAATCTCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT
upper sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 2
--------------gtcagtgttttctttctgcttcttctctca----atggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
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ttattctgtcaaatgataataactttgtcatataataatacacatgaaatgaatattatatagcggtattcatataacaatgcactacgcctttggtcagGTATGAAGGCCAGCGTGACATGCTGTACAATCAGACATTCAATCTCGATCAAGTTCAATTTGCAGCTGAAGGCATTAAAGATGCTCAACAAACT
upper sequence: AT5G04850.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
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taaaaatatctacggtctacctccactctccctacaaagtttccttttctattaat-tttatgttccacaatttaaggtca-ctccttatgcttttgctcagGTATGAAGGACAGCGTGACATGCTTTACAACCAAACATTCAACCTTGACCAAGTTTCATTTGCGGCTGAAGGAATTAAAGATGCTCAGCAAACTMapped 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|164130395|gb|ES113541.1|ES113541EST: GCAAAAGAAGAT GTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCA
genomic: GCAAAAGAAGATgtcagtgttt ... ttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
ttttaat putative branch site (score: 3)
ctgtttccatttttcc putative PPT
atatggattttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtgttttctttctgcttcttctctcaatggacattgatgatatggattttaataccaactgtttccatttttccttagGTATGAAGGACAACGTGACATGCTCTATAATCAGACTTTTAACCTTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG