Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G14740.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| | | | | | | | | | | | || || | ||||| | ||| | | | | | | | ||| | | || ||| |||||||||||| ||||||||||| || |||||||||||||||||| ||||||| ||| ||| | || || || ||||||||| |
-----------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctt---tatccatagcttatgacctgctaatattaatcccgtgtgctgtt--tctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G45380.1 (Glycine max), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| || ||||| || |||| || | |||| | ||| | | | ||| || || | | | || ||||||| |||||||||||||| ||||| |||||||| || ||||| || || ||||| |||||||||||| | || | || || || || |||||| || | || |||
----------------------------aaatcagaacacaagtgaatagtgatgattcatttgtaatttaacttattcagttttataggataaaaaattaatggtatttttgttggtggttttgcagCAATACATGGATTCAGAAATCAGAGCAATCATGGCGCAATATATGCCCTTGGACAGCCAAGCAGAAGTTCCAAATCATGTCAATGATCAAAGAGCATGAA
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
------------------------------------------gtaagcttttttaatctcttctgctctt---ttgttttctgttgtgtta-atagcgaa--gattaa-tcttgtat----------ttgccatatccgttacttggggaaaattgt-tttaacatt--------cctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| || | ||| | | ||| ||| || | | ||||| | | ||| |||||| | | |||| ||| | | | | | | ||| || ||| |||| | || || |||| ||| ||| ||||| || || ||||||||||| ||||||||||| ||||| |||||||||||| || || || ||||||| || ||| | || | |
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaactcaaatatgagaacatgacgtttgccatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------gtaagcttttttaatctcttctgctcttttgttttctgttgtgtta-atagcgaaga----ttaatcttgtatt-tgccatatccgtta----------cttggg-----gaaaattgt--tttaacatt-cctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| ||||||| || |||| |||| | | ||||| | | ||| | | ||| |||| | | | |||| || | |||| ||| |||| | | | || || |||| ||| ||| ||||| || || ||||||||||| ||||||||||| ||||| |||||||||||| || | || |||||| | || ||| | || |||
gtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaa-ttttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtatttttgttggtgtttttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAGTTGTAAATCACGTGCACGAAGAAAGAGCGTGAA
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 11
---------------------------------------gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
| | |||| | ||||| || || || ||| | | | | | || ||| | | | ||| || ||| | | | ||||||| |||||||||||||| || || || ||||| || ||||| || || ||||| |||||||||||| | || | || || || || |||||| || | || |||
gtaagctcttctgctttctctcattttggtggtgttattggatgcttaatgctgaaattctgtagcattagagcgtgctgagttgccgtcatgattcatttgtaatttaaatttattcagttttataggataaaaatttagtggtatttttattggtggttttgcagCAATACATGGATTCCGAAATTAGAGCAATCATGGCGCAATATATGCCCTTGGACAGCCAAGCAGAAGTTCCAAATCATGTCAATGATCAAAGAGCATGAA
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
|| | | || || | | ||| ||| || | |||||| | | |||| ||| |||| || | || | ||| || |||| ||| |||||||||||| ||||||||||| ||||||||||| |||||||| ||||||||||| | || |||| || || || ||| || | || |||
-------------------aatgttttaatgagttgagaaattgcaatg--taaggttgaca--atatttgttggttttgc-acttttggattattgatt-gatgtttc-atggt--tgctttttcagTCATACATGGACTCGGAGATCAGAGCTATAATGGCACAATACATGCCCCTGGACAGCCAAACGGAAGTCCCAAATCATGTCTCTGAGGATCATGCATGAA
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG-
|| |||| | | | ||| |||| || | || | | | |||| | || || || | |||| | | | ||| || |||| |||||||||||| ||||| || || |||||||| |||||||||||| | |||||| | || | |||| ||| || ||| |||
-------ttgcatgtctccacaaatggagatctctcttttgtactagtt-cgtaaagtg--cttgaacttatttgatt--------------aacggatttagcttgtcggtgct----gtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAA-GCGTAAAGAC
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGA-ACGCGCCTGAG
|||| | ||| | || | | | | | ||| || | | | | | | | || |||||||| || ||||| ||||| || ||||||||||||||||| | ||||||||| ||| | | ||||| || | || || | | ||
--------------------------------------------------------gtaatatca-attcgtgat-tgcttgatccagcaaaacttaacgttctctactggaaacttt--tcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGATGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-
upper sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 11
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGA-ACGCGCCTGAG
|| || ||| | || | || |||| | ||| || | | | | | | | || |||||||| || ||||| ||||| || ||||||||||||||||| | ||||||||| ||| | | ||||| || | || || | | ||
--------------------------------------------------gtaatatcaat-tcgtgctcgcttgatccagca-------aaacttaacgttctctactggaaacttt--tcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGACGTGCATCACCACTTGCAAGAGGATGCTTGATTGT-Mapped 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|116457029|gb|EG499621.1|EG499621EST: TGGGACTTGCAGCTGCTGGTGCATACCTCGTTTACAAATATAGGCTAAGG CAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTG
genomic: TGGGACTTGCAGCTGCTGGTGCATACCTCGTTTACAAATATAGGCTAAGGgtaagctttt ... ggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
ttttaac putative branch site (score: 2)
aaaattgttttaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC