Sequence
atgc intronic sequence ATGC exonic sequence...ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20890.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
ggaatgttgatagtcatcatgtcatcttgttgtg-----ttgtgtttcttcttctatcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
||| || | || | || ||| | ||| | | | | | ||| || || || | || ||| | | |||||| ||||||||||||||||| || ||||||||||| |||||||| |||||||| || || || || || || ||||||||||| || |||||||| |||
---ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgaca-ctgatatctttttttatttgcttct-tatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 7
----ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatcgagtaatatggtctcatgtcacctcaacttaaa-atctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
||| | ||| ||||| ||| | ||| |||||| | | || | | | || | | | || | | | || || || ||||||||||||||||| || || |||||||| ||||| || |||||||| || || || || || || ||||||||||| || |||||||| |||
gagtacaatttattgagtgttcatg-catgcatctatgtaatgtttcc----caacagaaaatggtcctaatatcttttttttatttgcttgtttctatttgcagATTCATTCTTGACAAGAAAATTGGCATCGGGCAGCCAAAGCGGATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatc-----gagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
| || ||| || | | | || | | || || | || ||| | |||| | || | || || || | | || || || ||||||||||||||||| || ||||| || || ||||| |||||||||||||| || | || || || ||||| ||||| || || |||||||||
--tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaa-agtaagctttctttctgtttttaattttttgatc--agATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 9
ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatcgagtaatatggtct-catgtcacctcaacttaaaatctatgcctgt-agGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
|| || || | | | || | || || | ||| || | | | || || |||| | | || || || ||||||||||||||||| || ||||| || || || || |||||||||||||| || | || || || ||||| ||||| || || |||||||||
--tgcattagtaatcttgttatttattttccaagcattgcttatccttgcattactctgggtaaaaagtaagctctgtctgttttaaatttgttttggtcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAACGTATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
---ggaatgttgatagtcatcatgtcatcttg-ttgtgttgtgtttcttcttcta-tcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
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cattctatattc-caactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagtaaatt--ttttttgttaattggaatcttgttttctgc--atagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAGMapped 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|116444514|gb|EG487106.1|EG487106EST: ATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG GTTTATTCTTGACAAGAAAATAGGAATTGGGCGGCCTAAGCGCATAGAGAA
genomic: ATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaac ... atgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctatcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
aacttaaaatctat 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
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ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaaa