Sequence
atgc intronic sequence ATGC exonic sequence...tctttattctttttcgttcatataagagccttccatggtagttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25490.1 |
intron # | 5 |
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 5
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
------------------------tctttattctttttcgttcatataagagccttccatggt----agttctatgtttgtacatgtatctttttatt---ttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
|||| || | | || || | || | ||| |||| ||| ||| || | || || || | | | | | ||| | |||||||| || |||||||| | | || | || ||||||||||||||||||||||| || || |||||||| || |||||||| || | ||
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
---------------tctttattctttttcgt-tcatataagagccttccatggtagttct---atgtt-tgtacatgtat---ctttttattttgacacaatttatgttataatatct----ctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
|| |||| | | | | | || | | | |||| | | |||| | || ||||| | | || | | || | | | ||| | |||||||| || || ||||| | | || | || ||||||||||||||||| |||||||| || |||||||| || ||||| || || | ||
gtattatttgtcctagctgaattcaacctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 5
--------tctttattctttttcgttcatataagagccttccatgg--tagttctatgtttgtacatg-----------tatctttttattttgac------acaatttatgttataatatctc----tagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
|||| |||||| | | | || | | ||| | || | ||| |||||| | | | | |||| || ||| | || | | |||| ||| |||| |||| ||||| | | || | |||||||||||||||||||| || ||||| || |||||||| || || ||||| | ||
gtgttcaatcttctttctttatgttaaaaatgattctttgacataaattgattattgctttatacatggaaagattaatcaacataatgccatgactcgtttactattgagaccattgccttttataatagGGGTGATCTGGTGTCAGCGTATGTTCGCCTTCTCTGTGACAATGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 5
tctttat-tctttttcgttcatataagagccttccatggt--agttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
| | || | |||| || || | | | || || | | | || | | | | ||||| | ||| ||| | | | || ||||| ||||| || || |||||| | ||||| | || ||||||||||||||||| |||||||| || ||||||||||||||||| || ||| ||||
taatcatgtgatttttgtattgattatctcttatgattactaaggcccaactctgaagcctaagcaatatattt--atttttctta-actattgtttatgaagAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGAGATAATGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 5
tctttat-tctttttcgttcatataagagccttccatggt--agttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
| || | |||| || || | | | || || | | | || | | | | ||||| | ||| ||| | | | ||| ||||| ||||| || || |||||| | ||||| | || |||||||||||||| || |||||||| || ||||||||||||||||| || ||| ||||
aaatcatgtgatttttgtattgattatctcttatgattaccaaggcccaactctgaagcctaagcaatatattt--atttttctta-actattgtttgtgtagAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGTGATAATGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
tctttattctttttcgttcatataagagccttccatggtagttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatc-tctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
|| ||| | | | || | | | | || |||| | || || | | ||| || || | ||| || | | || ||||| |||||||| || |||||| | ||||| | |||||||| |||||||| || || ||||| || || |||||||||||||| || ||| | ||
-attgatttcctcttatatttacgaaggtccagattcagtgtcctataaatttaactggttatgtttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTAMapped 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|86067631|gb|DR363388.1|DR363388EST: GCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAG GACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGA
genomic: GCTAATCAGCTATATGAACTTTGTGAGGCAGTGGGTCCTGATTGCACGAGgtatgtgttt ... atatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttgtacatgtatctttttattttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
ttttgac putative branch site (score: 3)
tatctct putative PPT
tatctttttattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttattctttttcgttcatataagagccttccatggtagttctatgtttgtacatgtatctttttattttgacacaatttatgttataatatctctagGACGGATTTGGTTCCAGCATATGTGAGATTGCTAAGGGACAATGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTG
- - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaat