Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaacaagaaaaactcggtcttaaacgagcatcgtccattccgatgtctaataaaatatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27640.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 10
gtatgtaa--caagaaaaactcggtcttaaacgagcatcgtccattccgatgt-ctaataaaat--------atttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
||||| | || | | | || ||| |||| | | | | | ||| |||| | || | |||||| |||||||| ||||| || || | |||| | || |||||||| ||||| || |||| ||||| |||||||||||||||||| ||| |||||
gtatggaggttccatcctacccttttctggactctcatgtctcattgctttacaccattgtaatcctttgtcatttactttaatttactggtacagTTCCTGTGGCGTCCGAGACCACCGTCGCTGCTGACCCCTGAAAAGGAAGACGAGATTGCGAAGAACCTGAGGAAGTACAGCAAGAAGTACGAGCAAGAGG
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 10
gtatgtaacaagaaaaactcggtcttaaacgagc---atcgtccattccgatgtctaata----aaatat-ttgtgtatgg-----ttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
||| | | | ||| | | | || || | || | ||||| | || ||| || | |||| ||| |||||| ||||| || ||||| || ||| | |||| || ||||||||||||||||| ||| || |||||||||||| ||||||||||| || ||| |
gtaaatgttcaatcattctccttttggatgcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggtggtacagTTTATATGGCGCCCGAGACCGCCCTCACTACTGACGGCCGAGAAGGAAGAAGAGATCTCAAGGAACCTGAAGAAGTATAGCAAGAAGTACGAACAAGAAG
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 10
-----------gtatgtaacaagaaaaactcg---gtcttaaacgagcatcgtccattccgatgtctaataaa-atatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
|| || | || | || | || | | ||| | || | || | || || | | | ||| | || | |||| ||| | ||||| || ||||| ||||||||| | ||||| || |||||||| ||||||| | ||||||| ||||||||||| || |||||||| |
ttgttgctgtagtccttattattgctaatctgcatgtttaccactgaatgcctttattgtgtaatcaactacacattcttattttttgtttgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCGGAGAAAGAGGAAGAGATTGCAAAGAACTTGAAGAAATACAGCAAGAAATACGAGGCAGAAG
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 10
-------gtatgtaacaa-gaaaaactcggtcttaaacgagcatcgtccattccgatgtctaataaaatatttgtgtatg-------gttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
| | | || ||| || | | | | || | | | ||| | | ||| | | || ||| | || | |||| ||| | ||||| || ||||| ||||||||| | ||||| || |||||||| || |||| | ||||||||||||| ||||| || |||||||| |
aatctgcatgtttggcactgaatgcctttattgtgtaataatcctgtgctagtcattcatcaatcacacattcttatttgttttttcgtttgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAAGAGATTGCCAAGAACTTGAAGAAGTACAGTAAGAAATACGAGGCAGAAG
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 15
--------------------------------------------------------------------------------------------------gtatgtaacaagaaaaactcggtcttaaacgagcatcgtccattccgatgtctaataaaatatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG---
| | || | || || | | | | | || | | | |||| || | | || | || | |||| ||| | ||||| || ||||| ||||||||| | ||||| || |||||||| || |||| | ||||||||||||||| || |||||||| |
gtaatgctccatttttgaatctatgttttggtagtataaatttttgtaatagcagaatttactcagcattgaaatctgcatgttatttggcactcaatgcctttattgtgtaattctgtgctagtcatttgtgtggatacttatcaatcacactttcgtattagtttttcttttgctatatagTTCTTATGGAGACCAAGGCCGCCATCTTTCTTGACTCCTGAGAAAGAGGAAGAGATTGCCAAGAACTTGAAGAAGTACAGCATA---TACGAGGCAGAAGATC
upper sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 10
------gtatgtaacaagaaaaactc--ggtcttaaacgagcatcgtccattccgatgtctaataa------aatatttgtgtatggttggt-tacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
|||| | ||||| | | | || || || | | |||||| | | ||| | | |||| | | |||||| ||||||||| |||| ||||| ||||||| | | ||||| || |||||||||||||||| | |||| |||||||| |||||||| ||||||||||
atacaattatggtgtagaaaaaaattctgaattcaatagatcacatggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGGMapped 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|86060060|gb|DR355817.1|DR355817EST: CTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCATTTCTTCCAG TTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAA
genomic: CTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCATTTCTTCCAGgtatgtaaca ... ggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAA
EST:
gi|125052611|gb|EL124286.1|EL124286EST: CAACGGGATTATGCTTTACCGGATATTGAAGGATCATTTCTTCCAG TTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAA
genomic: CAACGGGATTATGCTTTACCGGATATTGAAGGATCATTTCTTCCAGgtatgtaaca ... ggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcatcgtccattccgatgtctaataaaatatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
gtctaat putative branch site (score: 3)
tctaataaaatatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaacaagaaaaactcggtcttaaacgagcatcgtccattccgatgtctaataaaatatttgtgtatggttggttacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT