Sequence
atgc intronic sequence ATGC exonic sequencegtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55150.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 8
gtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
||| || | || || | || || | | || | || || |||| || || | | || |||||| || || ||||| || ||||| || ||||||||||| || |||||| |||||||||||||||| | ||||| ||||| || ||||| || || |||||
gtatacaaaaatcctcccagatcgatg--------aattatatttatttctgt---aaactaatgccacttatatctgg---aaacagATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGGAGGATTATGTTCATCGCATTGGTCGAACTGGCAGAGCTGGAGCAAAAGG
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 8
gtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaacaacagttctttttgttttg---aacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
| | | || || | | | | | ||||| | ||| | | ||| | | ||| ||| |||||| || || |||||||||||||| || ||||||||||| || || ||||| |||||||||||||| | || || ||||| || ||||| || || |||||
----------gtatgcccaactttg---agatgtgatacatcttatatttcctgaggaaattgatacacgtttctttcccttggaaaacagATGTCAAGGATGTGAAGTATGTCATTAACTATGACTTTCCGGGGTCACTCGAGGATTATGTTCATCGTATAGGTCGAACTGGCAGAGCAGGTGCAAAAGG
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 8
------------gtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaa-caacagttctttttg-ttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
| | | ||| ||| | | ||| || ||| | | ||| | | || |||| || | |||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||||||||||||| | ||||| || ||||| ||||| || || |||||
gtgatttgatgactttcagtttactttgtcactttttaaagttaaccaatagctttgcttatgt--atatcttaatcctttctactatttgattacggtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCCGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGACAGGGAGAGCTGGTGCAAAAGG
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 9
---------------gtactaaatctttttctcatctgcgtgcaaacatcaactct-cttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
| | | || | | | | || || | || | |||| || || || | || || || | | |||| ||||| |||||||| ||||| ||||| |||||||||| || ||||| |||||||||||||| | ||||| || | ||| ||||| || || |||||
gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaatagctttgcttatgtatatcttcatcctttctactatttgattactgt----cagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 8
-------gtactaaatctt--tttctcatctgcgtgcaaa---catcaactctcttaaccatggtgacaagctaa-caacagttctttttg-ttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
| | | | | ||| | || | | ||| ||||| || |||| | | ||| | | || |||| || |||| ||||| ||||| || ||||| |||| ||||||||||| || ||||| |||||||||||||| | ||||| || ||||| || || || || |||||
ttgtgatttgatgactttcagtttattgtcagtttttaaagttaatcaatagctttgctcatgt--atatcttaatcctttctactatttgattactgtcagATGTGAAGGATGTAAAATATGTTGTAAATTATGACTTCCCGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGACAGGGAGGGCTGGTGCAAAAGG
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 8
----gtactaaatctttttctcatctgcgtgcaaacatcaactctct-taaccatggtgacaagctaacaacagttct-----ttttgttttga--acagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
| || | || | | | | || || | | || | | ||| | | || |||||| |||| || || |||||||| | |||||| |||||||||||||| ||||| || || |||||||| ||| | ||||| |||||||| || || ||||| |||||
tgacatggctaaattcttgaaaggaagtgagagcatgtccacccaggatgacttcaaaagctgcatttcaatcttcttacatgttaggttttggttgcagATGTCAAGGATGTGAAATTTGTGATCAACTATGACTTCCCGGGATCTCTTGAAGATTATGTCCACCGCATTGGTCGAACAGGAAGGGCTGGGGCCAAAGGMapped 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|116454672|gb|EG497264.1|EG497264EST: AGGCAAAAGCCCTATAATGACTGCTACAGACGTTGCAGCTCGTGGATTAG ACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGG
genomic: AGGCAAAAGCCCTATAATGACTGCTACAGACGTTGCAGCTCGTGGATTAGgtactaaatc ... ttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaactctcttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
agctaac putative branch site (score: 2)
ttctttttgtttt putative PPT
tttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT