Sequence
atgc intronic sequence ATGC exonic sequence...ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75440.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 4
ttttgcttttagatccaag--ggtaca-ctcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
|| | | | | | ||| | | || | | | || |||| || | | || | | | || || | | || |||||||||||||||||| |||||||||||||| ||||| ||||| ||| |||| || || ||||| || ||| | || || ||| | | ||||
gaatggaaggaaaacaatgttggtgtagccttgatggccatggactacagtttactgtatgatttgtgattatcggctttc-tgctgcctcttgtc--tgcagATATTTTGTATGACTCGTGGTCTCCAGCGATGACCGTGAGCTCTGTCTGTATCAGTATCCTGTCTATGTTGTCTAGTTCGCCAGCAAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtat-ctgatg--ttgtgtatcatcgt-tgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG-----------
||| | | | |||| ||| || | | || | | | | | || | | | || |||| ||| | | | || |||| | ||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| || ||||| | || ||||| || ||||| | | ||||
tttggatgtaagat--aagactaatccctgatagc--tgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtat-ctgatg--ttgtgtatcatcgt-tgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
||| | | | |||| ||| || | | || | | | | | || | | | || |||| ||| | | | || |||| | ||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| || ||||| | || ||||| || ||||| | | ||||
tttggatgtaagat--aagactaatccctgatagc--tgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G116840_T06 (Zea mays), 3'ss of exon 3
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaaga-agtatctgatg-ttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG-----------
| | | || |||| | || | | | || || || ||| ||| | | |||| || || || | | | ||||||| ||||||| |||||||| ||||| ||||| || ||||||||||| || ||||| | || ||||| || |||||| | ||||||
-tgtacgacta-atccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGGTTACATATTT
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 5
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaaga-agtatctgatgttgtgtatcatcgt-tgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
| | | || |||| | || | | | || || || ||| ||| | | |||| || || | | | | ||||||| ||||||| |||||||| ||||| ||||| || ||||||||||| || ||||| | || ||||| || |||||| | ||||||
-tgtacgacta-atccttgatagttgacatttctaatcagttttttttttgccatgaaaatgggatattctagtaactattgattcctccacttacctacagATATACTGTATGACTCGTGGTCCCCAGCGATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
--ttttgcttttagatccaagggtacactca---aatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
|| | ||| | ||| | | | | | || || | | ||| | | | | | | | | |||| | || | | | || |||||||| | |||||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||||||| | || ||||| |||| |||
ggttcttatttcaatcccattattttatcaactgattctctgtggttgattgtccatc--aacacactgacatctaatatcatagcttatttgttttca---cagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
ttttgcttttagatccaagggtacact-caaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttg---cagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
| |||| ||| || | | | | | | | | | || | || | | || | ||| | ||| ||||||| |||||||| || ||||| ||||| ||||| ||||| || |||||||| ||||||||||| ||| | || || || || | |||
----aatcatagaatgaagaacactcgacgcagtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctgg--aaga--agtatctg-atgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
| || | | | | | ||| || || || | ||||||||| | | |||| | | |||| | | | || | |||||||| | ||||| || ||||| ||||| ||||| ||||||||||||||||| |||||||| |||||| | || || || |||| |||
--acgagttcccaacttaacgaaaact---atctctgtgtacttgaatttaacatgttgcgtttaattaagactaatttctgcaaacttggcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ21480 (Selaginella moellendorffii), 3'ss of exon 4
------------ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
| | | | | | | ||| | ||| | | || | || | | || | ||| | ||||| || | | |||||||| | |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| || | |||
gtgaagctttctctctctctcttttttttttacttctctccagccgtgatagatcttgatggatgatcgac-tcaaacttttcatttcttcttgtgtgtgtccttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
upper sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
| | | | | ||| | | ||| | | || | || | | || | ||| ||| |||| | | | |||||||| | |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| || | |||
--------gtgaaccttt--cttctctccagccttgatagatcttgatggatgattgac-tcaaacttttcatttcttttgt-gtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGMapped 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|86078444|gb|DR374201.1|DR374201EST: TCCAGCTCCTCTGCATCCTCACATTTACAGCAATGGGCATATTTGTCTAG ATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCA
genomic: TCCAGCTCCTCTGCATCCTCACATTTACAGCAATGGGCATATTTGTCTAGgtatgtcact ... atcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -gatccaa
- - - - - - - - - - - - actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - aacatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaag