Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaagtgcgttatacagtgattgc---tttatgcattggttcat-ctctgacagaattggtatttatcttaactat---gcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
||| || | | | ||| |||| | | ||||| | | | || | |||||| || | ||||||||||||||||||| || | ||||||||||||| |||||| || ||||| |||||||| || || |||||||| ||||| ||||||||||| | ||
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
-----gtaagtgcgttatacagtgattgctttatgcattgg--ttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| ||| | ||| | || |||||| | || |||| | | ||| | | || | | |||||||||||||||||||| | | || ||||| |||| ||||||||| ||||| ||||| || || ||||||||||| ||||| || |||||||| | ||
gttagttttttgcttcataaaatg-ttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
-----------gtaagtgcgttatacagtgatt----gctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
|| ||| | | | | || || || | | | ||| || | || | ||| | ||| |||||||||||||||||| | || |||||||| | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| ||||| | ||
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
-----------gtaagtgcgttatacagtgattgc-------tttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
|| ||| || | | || | ||| | | | ||| || || | |||| | | |||||||||||||||||| | || |||||||| | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| ||||| | ||
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
-----------gtaagtgcgttatacagtgattgctttatgcattg-gttcatc-tctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| | | || | || | | ||| || || ||| | || ||| || || | | |||||| || ||||| |||||||||||||||||||| |||| ||| ||||| ||||| |||||||| || ||||| ||||| ||||| |||||||||||||||||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttc-cattgattttta-tgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
-------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtat--ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| | | | | ||| ||| | | || || | | | || ||||| | || ||||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtatttatcttaact----atgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| | | | | ||| ||| | | | || || | | | || ||||| | || | |||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattg----gtat-------ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
||| | || | || || | || | | | || | |||| ||| || ||| | |||||| || ||||| ||||| |||||||||||||| |||| ||| ||||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||||||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
------------------gtaag--tgcgttatacagtgattgctttatgcattggttcatctctgacagaatt--ggtatttatcttaactat-gcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
||| ||| || || ||| | || ||| | | | | ||| | | ||| | | || | |||||||| || || |||||| | || |||||||| || | ||||||||| ||||| ||||| || || ||||||||||| || || || || || || || ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| | | | || |||| | || || || | | ||| | ||||||| || ||||||||| | ||||||||||| |||| || || |||||||| ||||||||||||||||| || || || || || ||||| ||| | ||
--------------------gtatgtggttaaatgtttcaacgttgccactttttgacacttgcttggc---acagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
| |||| | || || || | | ||| | ||||||| || ||||||||| | ||||||||||| |||| || || |||||||| ||||||||||||||||| || || || || || ||||| ||| | ||
----------------------------------gtttcaacgttgccactttttgacacttgcttggc---acagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTATMapped 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|116473629|gb|EG516221.1|EG516221EST: GTTATTCAACAAGGGAGATTGGCAGAACAGAAAA CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: GTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST:
gi|116473628|gb|EG516220.1|EG516220EST: AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST:
gi|125181844|gb|EL197762.1|EL197762EST: GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAAACAGAAAA CTGTCAATAAGGATGAGTTG
genomic: GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAA-CAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
tcttaac putative branch site (score: 2)
tatttatcttaactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT