Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaaattatacccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10030.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 8
---------------------gtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggc----ccctaaattatacccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
|| || | || ||| | || || || ||| |||| | || ||| | || | ||| ||||| | |||||||||||||| || |||||||| || |||||||| |||||||| || || ||||| | || | | | |||| |
gtaatcatgagtacttttctgaatggttttagtgtgacaattatgg-gtgatatttctaatcttttgtctaagtttattctgtatattgtgtcccctaaagGTATGGGTTCTTGATGCTACTCCTGGCAAGGTTCGTGCTGGGGGAGATGGCGAAGATCACCCTGCTGAACTTATTGAGTCCCTCAGAAGAATGCCTATGC
upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 8
----------------------------gtaagtgt--ttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaa-attatacccaatttagGCT-TGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
|| |||| || |||| | || | ||| | ||||| | | | | | ||| | | | | | ||||| | |||||||||||||| |||||||| || || |||||||| |||||||| || || ||||| |||||| | | | |||| |
gtgagctctacttcttgttttgaatgttgttggtgtaattgaaatatgtttgcattgattagttcttctctgttatgcttattttcttgatattctgtttcttaaaagGTATGGGTTCTTGATGCTACTCCTGGCAAAGTTCGGGCCGGGGGAGATGGTGAAGATCACCCTGCTGAACTTATTGAATTTCTCAGAAGAATGCCTGAGC
upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 8
-------gtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaaattat---------------acccaattt--agGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
| ||| || | ||| | | | | | | ||||| | || || |||| | || | |||| |||||||||| ||||||| || ||||| |||||||| ||||| ||||||||||||||||||||| ||| || ||||| |||||| ||| | ||||||| |
gttgacaaggattgtaaatatagtttctgtcttcttgtttcactgtattatatgtgagtgcttcttaattgtttcatacttgcttctacgctatttgaagGCTTGGGTTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGCAGAACTCATATCCTTTCTAAGTACACTGCCAAATG
upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G44190.1 (Glycine max), 3'ss of exon 8
--------------gtaagtgtttatccgatgtctatatcgcaatgttggt-----agggtttat--gttaaggc-ccctaaattatacccaattt--agGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
|||| | | | | | | | | | || | |||| |||| || | | || || || | |||| |||||||| | ||||||| || ||||| |||||||| ||||| ||||||||||||||||||||| ||| || ||||| |||||| ||| | ||||||| |
aaggattgtaatttgtaactatagtttgtcttcttgtttgcctgtatttatatgtgagggcttattaattgtttcacacttgcttctatgctatttgaagGCTTGGATTCTGGATGCAACCCCTGGAAAAGTTCGAGCAGGTGGAGATGGAGAAGATCATCCAGAAGAACTCATATCCTTTCTAAGTACACTGCCAAAGG
upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------gtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaaattatacccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
|| ||| || ||| | | || | ||| | || | ||| ||| | ||||| |||||| | ||||| |||||||| ||||||||| | || ||||||||||| ||||||||| || || ||||| || || ||||| |||| || |
ccagaactggtaatcttcatgaaatttgaattgtggttcaagcaattatgatctattattctttttttttttttttaattttataatctattttta--ttagGTTTGGGTTCTAGATGCAACTCCTGGGAAAGTTCGTCCTGGTGGAGATGGAGAGGATCATCCAGAGGAACTAATATCTTTCCTTAGTAAAATGCCCAATGMapped 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|164228584|gb|ES103869.1|ES103869EST: AAGCCTCTTCCACGACCAGTCCGA GCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGG
genomic: AAGCCTCTTCCACGACCAGTCCGAgtaagtgttt ... cccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatcgcaatgttggtagggtttatgttaaggcccctaaattatacccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
ccctaaa putative branch site (score: 3)
taaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtttatccgatgtctatatcgcaatgttggtagggtttatgttaaggcccctaaattatacccaatttagGCTTGGGTATTGGATGCTACTCCTGGTAAAGTTCGTGCAGGAGGAGATGGAGAAGATCATCCACGAGAGCTTATATCATTTCTACGTAAATTGCCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT