Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20890.1 |
intron # | 4 |
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 4
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------------------gtatgtaat-ttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagtt---------cgttgtatct-ggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
||||| | | || | | ||| | || || | || || || || | ||| | || ||| | || | || | ||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||||| ||||| || |||||| |||||||||| |||||| | || |
gtatcctttaatttgacccttttttattgctacaccggttaggtaatatcactgttttaaatctctgtttcatatgtatgaagtgttttttacttcatatttttgataatttattggatc---ttcttgttggccaatctttataatgcaaaaataaaaaaaagttattccttaatgtgggcctcagACATCTCAAAAGTGCAAGATGACGAAGTAGGTGATGGAACTACTTCTGTTGTTGTTTTGGCTGGTGAGCTTTTGAGGGAAGCTGAAAAGTTGGTAAATAT
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------------------gtatgtaatttccct-------gcgacattctggcatgaagttt-tcacat----tcgttt---tttcttagttgggttttctctcacagttcgttgtatctggtttgt-tcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
| || || ||| || |||| | | | ||||| ||| || ||| | | | | || | | | ||| || ||| || | | | ||||||||| ||||||||||||||||| |||||||| || || |||||||| ||||| ||||| || || ||| ||||||| || |||||| | ||
gtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatca-aggaagttaagtccttaacgcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGGTTGTTTTGGCTGGAGAACTTTTGAGGGAGGCTGAAAAGTTAGTTAACAT
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 12
gtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC-----------------------------
|| | | | |||| || | ||| | ||||||||| ||||||||||||||||| ||||||||||| || || ||||||||||| | || || || ||| ||| ||| || || ||| | |
-----------------------------------------------------ctaatgaaaga-------aaggccagttgctccttaatggttgct-agacatctcaaaagttcaagatgatgaagttggtgatgggacaacttctgttgttgttctagCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 3
-----gtatgtaatttccctgcgacat--tctggcatgaagttttcacattcgtt-ttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
| || | | | || ||| | | |||| | | ||| || ||||| || | | || | || || | | || | ||||||||| ||||||||||||||||| ||||||||||| || || ||||||||||| | || || || ||| ||| ||| || || ||| | |
ttaaacttcatattctgcttgtgacctcatttggcccctcttctgtacaaatattattttcctaatgaaag--------aaaggccattactccttaat-gatcattagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACAT
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
-----gtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
|| | |||| |||| || | | || || | | | ||| || || ||| ||| | | ||| ||| | |||||| || ||||||||||||||||| ||||| |||||||||||||| |||||||| ||||| || || ||| | ||||| ||||||||||| || || |
tcaccgtttataata--cctgtcctgttattaattagagcattgatgtggatctttctttgcatg---tttaaatcataagataat-catccttaatgtaagttagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 5
-----gtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
|| | |||| || | | | | | || | || | ||||| || || ||| ||| | ||| || | |||||| || ||||| ||||||||||||||||| |||||||||||||| |||||||| ||||| || || ||| | ||||| ||||||||||| || || |
tcactgtttttaatacccgtccagt-tattaataaga-gcattggtgtggatttttctttgcatg---tttaaatcataagataac-catccttaatgcaagttagACATATCAAAAGTACAAGATGATGAGGTTGGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGC
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtaatttccctgcgacattctggcatgaagttttcacattcgtttttt---cttagttgggttttctctcacagttcgttgtatctggtttgttctt----cagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
|||| | | | | | | | ||| |||| | | | | || |||| ||| | | | || | || | || ||| |||| || || ||||||||||||||||||||||||||||| || || || |||||||| ||||| || |||||| | || |||||||| ||| | ||
gtatagatgtgaaatacaaagccat--ctggaactttttataacccatgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------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|116444514|gb|EG487106.1|EG487106EST: CACATAGACAACCCTGCAGCTAAAGTTCTTGTTG ACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTG
genomic: CACATAGACAACCCTGCAGCTAAAGTTCTTGTTGgtatgtaatt ... tgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
ctctcac putative branch site (score: 3)
tttgttcttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaatttccctgcgacattctggcatgaagttttcacattcgttttttcttagttgggttttctctcacagttcgttgtatctggtttgttcttcagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT