Sequence
atgc intronic sequence ATGC exonic sequenceTTCACCTGTAGGCCACTGGATTCCTGCACATGTGGATCACTACGGGTTGGGAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29160.3 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 9
TTCACCTGTAGGCCACTGGATTCCTGCACATGTGGATCACTACGGGTTGGGAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacaca-caatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacag
|||| | | | || | |||| | | |||| | | || | |||| |||||||| ||||||||||||||||||||||||||| | | |||| || | || || | || | | | || | ||| | |||| | | | |
TTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgttt-tgcatgatgttcctttttacttcttttgtaacacaccgaaatttgtac-tgacatatcaattatccaacag-------------------------------------------------------------
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 9
TTCACCTGTAGGCCACTGGATTCCTGCACATGTGGATCACTACGGGTTGGGAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtt--------tgttcctgattactgattctttttgttcctcaccataaagtcttctga-atgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacag
|||| | | | || | | || | | |||| | | || | |||| |||||||| ||||||||||||||||||||||||| ||||| ||||| | | |||||| | ||| || | | |||| | | ||| | ||
TTCAAATACAAGGCATTATCTCCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCCCACATTATCCTGTTGAAAGAAAATGGGCTCTTGGACTTCAGgtcttgcatgatgttctcttttact-actacttttgtgacacactgaaatttgtgctgacgtatatcacttatccaacag-----------------------------------------------------------------Mapped 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|47832194|gb|CK121878.1|CK121878EST: GAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAG TCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAA
genomic: GAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtttgttcct ... ttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCACCTGTAGGCCACTGGATTCCTGCACATGTGGATCACTACGGGTTGGGAGCAAGATCACAAGTCCCTGTTGATCGAAAATGGGCTCTTGGACTTCAGgtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacag
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA