Sequence
atgc intronic sequence ATGC exonic sequencegtagcctaaaatatgtctgctttgtcaatgtatccaggagttatgaaaatgttaacttggtgttaaaacatgtgttcttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 6
--gtagcctaaaatatgtctgct-ttgtcaatgtatccaggagttatgaaaatgt-taacttggtgt-taaaaca----tgtgttcttgttg----gcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
| | || | | | || |||| | | |||||| | | ||| || |||| | || |||| ||| | | || ||||||| |||| || || ||||| || ||||||||||| ||||||||| ||||||| || |||||| | || ||| ||| | | || ||||| |
cccttgtctcacttttacagtctattgttttatttttcaggagctgactagctgtataccttgtcatatataacaacattgtaacgtggatgccttgcagGTGCATCTAGTGGAGTGGCTCAAAATGATGGTTGGCACAAGAAGATCTGAAGAGGTAGTTGACCCTGACATGGAGGTCAAACCGACCATTCGGGCTCTTA
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 6
--gtagcctaaaatatgtctgctttgtcaatgtatccaggagttatgaaaa--tgttaacttgg--tgttaaaacatgtgttcttgttgg--------cagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
| | | || |||||| | || | | || ||| | | ||| | ||| | ||||| | | | ||| ||||| |||||||||| ||||| || ||||||||||| || ||||||||||| || || || || | || ||| ||| || || || |||||||
ccatttattgtggcaagtgtgctttctaaa-atttgcacgagcaacaattccttgtcagcttcgatcgttaataatcagctacaacatggagacggtgcagGTACATCTGGTCGAGTGGCTCAAAATGATGGTTGGCACGAGAAGAGCTGAGGAGGTGGTGGATCCTGACATGGAGTTGAAACCTGCCACTCGGGCTCTGA
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 5
-----------------gtagcctaaaatatgt----ctgctttgtcaatgtatcc--aggagttatgaa-aatgttaacttggtg--ttaaaacatg-tgttcttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA-
|| | | | | | || || | | | | | ||| || | | |||| ||||| | | || | || | |||||||||||||| || |||||||| ||||||||||| || ||||| || ||||| |||||||| ||||||||| |||| ||| | | ||||||| | |
tatgaaatacttaatcagtgctttcagctttctgcttctaacttctttgttttccatgaaaagtgatcaccactgtttgtatggtgaatgggattttgattatcctcatggcaggTGAATCTTGTTGAATGGCTCAAGATGATGGTGGGGACAAGGAGGGCTGAGGAAGTTGTGGACTCAAGGCTTGAAGTGAAACCATCAATACGTGCTTTAAA
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G42170.1 (Glycine max), 3'ss of exon 5
-----------------gtagcctaaaatatgtctgctttgtcaatgtatcc----aggagttatgaaaatgttaact-tggtg--ttaaaacatgtgt-tcttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
|| | | | | | | | ||| | | || ||| || | | || || | | | | | | || | || | || ||||||||||| || |||||||| ||||||||||| || ||||| ||| |||| |||||||| ||||||||| |||| ||| | | ||||||| | |
gtttgaaatacttaatcagtgcttccagtttactgattctaactttgttttcgatgagaagtgatcacagctttttctatagcgggtgagattttgattatcctcatgacagGTGAATCTTGTTGAATGGCTCAAGATGATGGTGGGGACAAGGAGAACTGAGGAAGTTGTCGACTCAAGGCTTGAAGTGAAACCATCAATACGTGCTTTAA
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 7
-------gtagcctaaaatat----gtctgctttgtcaatgtatccaggagt-----tatgaaaatgttaacttggtgttaaaacatg-tgttcttgtt---ggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
| | || || | || |||| || | || | || || |||| | | | || | | | ||||| || | ||||||| ||||| ||||| ||||| || ||||||| || ||||||||||||||||||||||| || ||| |||| | ||| | ||||||||||| |
gtatttctctgtccaatgcattggggacttctttctcctttcgtcgaaaggtaaatatacaggcttgttcaagaagagctatgataagctgttcatgctcatggcagGTTAATCTTGTCGAGTGGCTTAAAGTGATGGTAGGGACAAGAAGAGCTGAAGAAGTTGTGGATCCAAACCTTGAAGTTAAGCCCACAACACGTGCTCTAAMapped 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|124990525|gb|EL062794.1|EL062794EST: TATAACTGGAAGAGATCCAGTTGACTATGAACGTCCAGCTAATGAG GTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAG
genomic: TATAACTGGAAGAGATCCAGTTGACTATGAACGTCCAGCTAATGAGgtagcctaaa ... ttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaggagttatgaaaatgttaacttggtgttaaaacatgtgttcttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
tgttaac putative branch site (score: 2)
ttcttgtt putative PPT
ttatgaaaatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcctaaaatatgtctgctttgtcaatgtatccaggagttatgaaaatgttaacttggtgttaaaacatgtgttcttgttggcagGTGAATCTGGTCGAATGGCTAAAGATGATGGTTGGAACAAGAAGAGCTGAAGAAGTTGTTGACTCAAGGATTGAGCCTCCACCCGCTACACGTGCTCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT