Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03730.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctag-gtcctatttccaatggaagctaaataattactgactttgatata-------tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
| | | | ||| ||||| | | | | ||| || || | || | | || || ||| || |||| |||||||||||||||||||| | ||||||||||| || ||||| ||||| ||||| |||||||| || || ||| | |||||||| |||||||
------------------------gtaagttcatattaccgttacttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaata--attactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
|| || | | | | ||| ||| || | | | ||| | | ||||| | ||| | || ||| | |||| |||||||||||||||||||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || ||||| ||||||||| |||||||
----------------gtaagttatattgttccgtttagtgta-ttttgttttgttacgcaattctat--gtggctaagtgttattctgtgccatgctatct-agCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G036902_T01 (Zea mays), 3'ss of exon 1
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaataat----tactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
|| | | | | || || || || | || || || || | | | | ||| |||| | ||||||||| || ||||||||||| ||||| || |||||||| || || ||||| || || ||||| || |||||||| || ||| | ||||| || ||| |||
-----------------------------gtaagagcctcttcaactttttttaagttcccctttcactgaaatttgccttgtataatcctgtcttttaaatatcagCCTGAATGGATGGCACCTGAAGTGCTTCGAGATGAACCATCCAATGAGAAATCTGATGTCTATAGCTTCGGTGTTATCCTATGGGAACTAATGACACTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 13
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctattt-ccaatggaagctaaataattactgactttgatata-tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
|||||| | ||| |||| | | | | | | ||| | ||| | || || ||| | ||| ||| | || | |||| ||||||||||| |||||||| || || |||||||| || ||||| ||||||||||| |||||||| || ||||||||||||||||| || |||||||
gtaagtatacttt---caaaacgtgtatcttccttttgaatcgtttgattcagatgtcatttttattattgcaaattaagttga-actcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGATGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 13
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttcca---atggaagctaaataattactgactttgatata-tcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
||||||| | ||| |||| | || | | ||| || || | | |||| | || || ||| | ||| ||| | || | |||| ||||||||||| |||||||| || || || ||||| || ||||| ||||||||||| |||||||| || ||||||||||||||| | || |||||||
gtaagtttacttt---caaaacgtgtatcagccttttgaattg--tttgtttcagatgccatttttatttttgcaaattaagttga-actcctttttctctacttagCCTGAGTGGATGGCTCCAGAAGTTCTTCGTGACGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
gtaagttcagtttgtttgaaactaaaac-acgctgaacaacgtaactttcttctaggtcctatttcca-atggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
||||||||| ||| || | | | || || || || |||| | || ||| | | | ||| | || || ||| | | |||| ||||||||||| ||||| || || || |||||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcag--aagttttataactacgtttttattaatt--tttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 12
gtaagttcagtttgtttgaaactaaaac-acgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
||||||||| ||| || | || | || || | || |||| | || ||| || | | | || || ||| | | |||| ||||||||||| ||||| || || | |||||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||
gtaagttcacattgactgcagatatttctgttttgtacgtcttatgtttcag--aagtaagttttataactatatttttaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTTGTGATGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
upper sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
gtaagttcagttt-gtttgaaactaaaacacgctgaacaacgtaactttc--ttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
||||||| | | | || | || ||| || | | | ||| | || | |||| || || | |||| || | ||||||| |||||||||||||||||||| || || |||||| | || |||||||||||||| | || ||||| || | ||||||||||| ||||| |||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcatttt-gtcacaaatataaaatttacatttttcatttcatcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGCMapped 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|116423837|gb|EG466429.1|EG466429EST: CGCGATTGAAGGCCAGCACGTTTCTTTCCTCGAAGTCAGCAGCTGGAACC CCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAG
genomic: CGCGATTGAAGGCCAGCACGTTTCTTTCCTCGAAGTCAGCAGCTGGAACCgtaagttcag ... gatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
aagctaaataatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcagtttgtttgaaactaaaacacgctgaacaacgtaactttcttctaggtcctatttccaatggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT