Sequence
atgc intronic sequence ATGC exonic sequence...ctttatatcaacccttcacatgagtgaccagtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G139700_T01 (Zea mays), 3'ss of exon 1
--ctttatatcaacccttcacatgagtgaccagtccttgttcggttctaaa-acagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
| | | | |||| | || | | ||| | | | | | || ||| || | | | | | | || |||||||| || ||||| ||||||||||||||||||||||||| | || | ||||| || ||||| ||||| ||| | || ||| | || || | || || ||
gtgagtgagtgagtgggttacatatacgtacatactctcgctggtgatgaccgtaccgatcacccgactatgatgatgatgatga-tgatga----tgagcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACTGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGCGGCCGGCTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G393433_T02 (Zea mays), 3'ss of exon 1
ctttatatcaacc-cttcacatg-agtgaccagtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
| | | | ||| | || | ||||| | | | | || ||| | ||| || | || | | | || || ||| |||| || ||||| ||||||||||||||||||||||||| || || | ||||| || ||||| ||||| ||| | || ||| | || || | || || ||
--gtgagtgagctgctttgcttgcatcgaccacccaccgattg-------aataga-----cattaagcttgtcgtgatgtgatgtgatctgatctgatcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACAGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGTGGCCGGCTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
-------------------------ctttatatcaacccttcacatgagtgacca-gtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
|| | | | || | || || | | || | || | | | || | ||| | | || | || | | ||| ||||||||||| || ||||| ||||| |||||||||||||||| || | ||| | || |||||||| || | ||||| || || || || |||||||| ||
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttgg-actttccacctcaccta-acctttgt--ttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G34950.1 (Glycine max), 3'ss of exon 1
----------------------------------------ctttatatcaacccttcacatgagtgaccagtccttgtt----cggttctaaaacagagtcc--tccttactctgtttgtaactttcac--ttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
||| | | || | || | || | |||| | ||| || || ||| || | | ||||| || || | ||| ||||||||||| || ||||| ||||| |||||||||||||||| || | ||| | || |||||||| || | ||||| || || || || |||||||||||
gtaaaattaagcactttcaacgccctttctttttttctttcttatctttggctattaatatttctt-tcattacttgctatagtggtagtacaaagaagtttggattttccacctaacgtaacctttgtggttgtttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGGAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGTTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
ctttatatcaacccttcacatgagtgaccagtccttgttcggtt---ctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
|| | | ||| |||| | | || || ||||| | | | ||| || | | || || ||| | |||| ||||| || ||||| |||||||||||||||||||||| || | || || || || ||||| || || |||| ||| | || ||||||||||| ||
-------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------ctttatatcaacccttcacatgagtgaccagtcc----ttgttcggttctaaaacagagtcctcc---ttactctgtttg---taacttt-----------cacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
| || | | |||| ||| || | ||| ||| | | | | ||| ||| | || || ||| ||| | | | || || ||||||||||||||| | ||||||||||| ||||| ||||||| || ||||| | || || |||||||| | |||| |||||||| || || || ||
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S327_64V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------ctttatatcaacccttcacatgagtgaccagtcctt---gttcggt-----tctaaaacagagtcctccttactctgtttgtaactttcacttataccatttga----gcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
| || | | | | | |||| | ||||| || ||| | | || | || | | | | |||| | | ||| |||||||||||||| | ||||||||||||||||||||||||| || | || || || || || |||||| || |||| || ||||| || ||| |||||
gtgacacaaactcccaatccttccagtatcatctggtgt-agtgtgctgtcctccgaatttggtgatcatgtgaactgagatggaccgaatcattgaaattagtttcctcggtgggaaatgatcttgcagAGAAAGCGAAGTTAGGGGAGAAGGAGTGGTACTTCTTCAGCCTGCGGGATCGCAAGTATCCGACGGGAATGCGAACAAATAGAGCCACCGAAAAGGGTTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S159_57V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------ctttatatcaacccttcacatgagtgaccagtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
|| | | | |||| | || | ||| | | | | | || | |||| | ||| ||| |||||| | | |||||||||||||||||||| || | ||| ||||||| || || ||||||||| | ||||| |||||||| || || || ||
gtatgcattgtttatttaaattaaattcaactttttaggatgctgcaccatggatttcattaggagtacaggatactgcggcaacactagattaattccttgaaaaacctttacagtacttgattcttgtttgttttctcagTGAAAGCAACGTTTGGGGAGAAGGAGTGGTACTTTTTTAGCCTACGAGACCGAAAGTATCCAACGGGATTAAGAACCAACAGAGCCACTGAGAAGGGCTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------ctttatatcaacccttcacatgagtgaccagtcctt---gttcggtt-ctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
|| || || || | | | | || | || ||| | || | | | || | | | | ||| || | | | ||||||||||| || ||||| |||||||| ||||||||||| | | || ||||| || ||||| ||||| || | ||||| | ||||| || || || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttctttttt-ctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA
upper sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------------------------------------ctttatatcaacccttcacatgagtgaccagtcctt---gttcggtt-ctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
|| || || || | | | | || | || ||| | || | | | || | | | | ||| || | | | ||||||||||| || ||||| |||||||| ||||||||||| | | || |||||||| ||||| ||||| || | ||||| | ||||| || || || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttctttttt-ctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTAMapped 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|86063971|gb|DR359728.1|DR359728EST: CGCCATTTCTCAAGTTGATCTCAACAAGTCTGAGCCTTGGGAGCTTCCTG AGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACC
genomic: CGCCATTTCTCAAGTTGATCTCAACAAGTCTGAGCCTTGGGAGCTTCCTGgtaagcccac ... atttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
ttgtaac putative branch site (score: 2)
tttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttatatcaacccttcacatgagtgaccagtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - -tcaaccc
- - - - - - - - - - - - - -ccagtcc
- - - - - - - - - - - - - - - - - - - - - - ctaaaac