Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaagaaaagacaattatccagtactaagctaatacttgaaattattatcacattctgtttctaaagtattaaaccttttcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19270.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G017845_T02 (Zea mays), 3'ss of exon 7
gtaagtaaagaaaagacaattatccagtactaagctaatacttgaaattattatcacattctgtttctaaa-gtattaaaccttttcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
| ||| | | || | | | || || || | || | | | || ||| | | || ||||| | |||||||| | || | || |||||||||||||| ||| | ||||||||||| |||||||| ||
-------------gtatgtttactatgctcaaaacccaaaatttctttttctaccccactgtactgttagctgtagctattttgtttcttttggataccagGGTCACCACCATCTTCCTGAAACAAGAGGACTATGCTTATCAGAAGAACAGACTGTTAGCACG-------------------------------------
upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 7
gtaagtaaagaaaaga-caattatccagtactaagctaatacttgaaattattatcacattctgtttctaaagtattaaaccttt-tcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
|||| || | || ||| || || | || | | | | || | || ||||| | | | | | | || || | | |||| |||||||||||||| ||||| |||||||||||||| ||||| || | | |
ccaagtcaacatgctttcacctatggagcttcaattcattatt--agttcaagattaaatagtgttttcccattttcatatttgagtctttatcttgggcagGGCCACTATCACATGCCGGAAACCAGAGGACTCTGCCTCTCAGAGGAGCTCAGCACT-------------------------------------------
upper sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 8
gtaagtaaagaaaaga-caattatccagtactaagctaatacttgaaattattatcacattctgtttctaaagtattaaaccttt-tcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
|||| || | || ||| || ||| | || | | | || || | | ||||| | | | | | | | || || | | |||| |||||||||||||| ||||| ||||| |||||||| ||||| || | | |
ccaagtcaacatgctttcacctatgaagctttaattcattatt--agttcatgattaaacagtgtttttccattttcatatttgagtctttatcttgggcagGGCCACTATCACATGCCGGAAACCAGAGGGCTCTGCCTCTCAGAGGAGCTCAGCACT-------------------------------------------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|116457268|gb|EG499860.1|EG499860EST: CCTTGGTTGAGAGACAAGCACTTAACGAAGCCAGAGAAGGTGAAAAGAAT GGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAA
genomic: TCTTGGTTGAGAGACAAGCACTTAACGAAGCCAGAGAAGGTGAAAAGAATgtaagtaaag ... tgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAA
EST:
gi|116457269|gb|EG499861.1|EG499861EST: CCTTGGTTGAGAGACAAGCACTTAACGAAGCCAGAGAAGGTGAAAAGAAT GGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAA
genomic: TCTTGGTTGAGAGACAAGCACTTAACGAAGCCAGAGAAGGTGAAAAGAATgtaagtaaag ... tgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattattatcacattctgtttctaaagtattaaaccttttcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
ttctaaa putative branch site (score: 2)
ccttttcattttgctt putative PPT
tttctaaagtattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaagaaaagacaattatccagtactaagctaatacttgaaattattatcacattctgtttctaaagtattaaaccttttcattttgcttcttagGGTCACTATCACATGCCAGAAACAAGAGGACTCTGCCTTTCAGAAGAACAAACTGTTAGTACTGTAAGAAAGCGATCAAAGCATGGCACAGGAAAATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA