Sequence
atgc intronic sequence ATGC exonic sequenceGGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35270.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G00240.1 (Glycine max), 5'ss of exon 2
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaa---aacttatagttattatgtctatctta--tcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag
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GGCGACAAGAGACGAACCAAGGCAGAGAAGACTATCAGCTTGCCAGTTCTTCGACAATACTTTGCAGGAAGCCTGAAAGACGCTGCCAAGAGCATTGGCGgtacgtaaattattaatttgcttcttcttcttcttctttaatttaatttctttgtttttgataactcgatcat----ttctgattgcgcgcag---
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G00210.1 (Glycine max), 5'ss of exon 5
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctc--tcagaaagtgatgattc-attcacgcagtttcattttcatgttgcag
|| || |||||| |||| || |||| ||||| || | || ||||||||||||||||||||||||||||| ||||| || |||||||||||||| |||| | | | | | || | ||| | | |||||| | | | | |||| | || || | | | | ||| ||||
GGCGACAAGAGACGAACCAAGGCAGAGAAGACTATCAGCTTGCCGGTTCTTCGACAATACTTTGCAGGAAGCCTGAAAGACGCTGCCAAGAGCATTGGCGgtacgtacgtaggat-gtattaatttgctttttcttatttgttttaatttgtttttgataactcgatcgatcctttctgattgcgcccccgcag
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G48080.1 (Glycine max), 5'ss of exon 1
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaat--ctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag
|| ||||||||| |||| || | || ||||| || | || |||||| | |||||||||||||||||||| |||||||| || ||||||||||| ||| ||| | | ||| | || |||| | || ||| | || | || || || | | | || ||| |||| |
GGAGAGAAGAGACGAACCAAGGCCGAGAAGACTATCAGCTTGCCAGTTCTAAGGCAATACTTTGCAGGAAGCCTAAAAGATGCGGCTAAGAGCATTGGCGgtgagatatta---tta-atttgatatgatccattaattaattgcattcctcatgtagctcttaatgaatg-aattgcatg--catgcag---
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA14G00470.1 (Glycine max), 5'ss of exon 2
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctct-cagaaagtgatgattcattcacgcagtttcattttcatgttgcag
|| ||||||||| |||| || | || ||||| || | || |||||| |||| ||||||||||||||||| |||||||| || ||||||||||| ||| ||| | | | | || | ||| | || || ||||| | | | || || || | | | | |||| |
GGCGAGAAGAGACGAACCAAGGCCGAGAAGACTATCAGCTTGCCAGTTCTAAGACAGTACTTTGCAGGAAGCCTAAAAGATGCGGCAAAGAGCATTGGCGgtgagatatgatccat-taataattgcattc--tttgtctctctctactccagctcttgtttaatgaatgaatgaatgcatgcatgcag---
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S302_9V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag---------
||| | || || || ||||||||| || || || | || |||| |||||||||||| || ||| | |||||||| |||||||||||||||||| || | | | | | | | | ||| || | | | || || | | | |||| |
CTTGATAGAAGGCGAGGAACAACAGAAAAAACGATCGGCCTCAGCGTCCTTCAACAATACTTTGCGGGTAGCTTGAAAGATGCTGCCAAGAGCATTGGTGgtcagtttgctcaatcctcttcagatcgaatgatctatacatgttgaaagccagatcgcttaatgagtgtcagagtagatgggtgttttggaaacttcta
upper sequence: AT4G35270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S250_18V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag--------------
||| | ||| || || ||| |||||||| || || | || |||| ||||||||| || || ||||| |||||||| |||||||||||||||||| || | | | | ||| || | | || ||| ||| | ||| ||| | || || || | |
CTTGATAGAAGACGAGGAACAACGGAAAAGACTATCGGCCTTAGTGTCCTTCAACAATACTTCGCGGGTAGCCTGAAAGATGCTGCCAAGAGCATTGGTGgttagttccctgaatcctc-tcattgtg---aattgctcgatccctctgggtgtgggagggcatagttatcaata-atgtttatagtccgaccgtgccttgtgcaMapped 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|125016680|gb|EL088949.1|EL088949EST: TCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTG TTTGTCCAACTACCTTGAAA
genomic: TCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaaga ... catgttgcagTTTGTCCAACTACCTTGAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGTGAGAAGAGAAGAACAAAAACAGAAAAGACAATTGGTTTAGAAGTTCTTCGACAATACTTTGCAGGAAGCCTCAAAGATGCAGCCAAGAGCATTGGTGgtaagaaagaaaacttatagttattatgtctatcttatcaatctctcagaaagtgatgattcattcacgcagtttcattttcatgttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA