Sequence
atgc intronic sequence ATGC exonic sequencegtacaacacaatctgacatagctatgtttgcaaatagactgatttctgattcatttaacgaagtttctactcaaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g12390.2 (Oryza sativa), 3'ss of exon 7
----gtacaaca-caatctgacatagct---atgtttgcaaatagactgatttctgattc-atttaacgaag--------tttctactcaaa--aaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
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actgatttgttagtaattgggcacattcaacaggcttagcgataaatcctttaccatttttattttgcgatgaaataactctactactctacttatatagGAATGGCCTGAGGAGAGTTATCCTCCATGGGCACATGGTCCGGGATACATTGTATCACAAGACATAGCAAAAGAAGTTTACAGGAAACACAAGAGAGGAG
upper sequence: AT1G26810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 7
-----------------gtacaacacaatctgacatagct-atgtttgcaaatagactgatttctgattcatttaacg-aagtttctactcaaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
|| ||| | ||||| | || ||| || | | | | | | | || | | ||||||||||||||||||||||| ||||||||||| || || ||||| || | ||||| | ||||| ||| | | | | || | |
tgcaaccagtcaccatactaagacaaaggggatcatagatgatatttttggatggtcaagaaacacaagtgctaactatgaattgtgatttgctctgcagGAATGGCCTGAAGAGAAATACCCACCATGGGCACACGGACCAGGATATGTGGTATCACAAGACATTGCAAAGGAAATCAACAGTTGGTATGAAACAAGTC
upper sequence: AT1G26810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G164072_T01 (Zea mays), 3'ss of exon 5
------------gtacaacacaatctgacatagctatgtttgcaaatagactgatt-tctgattcatttaacgaagtttctact------caaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
| | | | | ||| | ||| | | | || | | | || | | || ||| | | | ||||||||||||| ||||| ||||| |||||||||||||||||||| || ||||| || | |||||||| || ||| | | ||| | ||
ttaaagcatattttgctgccttgttttcaataatttagttccggttttgtcattttgtgcggtggatcaagtgtggtaactaatgttttgcttgagttagGAATGGCCTGAGGAGAATTATCCTCCATGGGCGCATGGTCCAGGATATATTGTTTCACAGGACATAGCTAAAGAAGTTTACAGGAAACACAAGAATGGGG
upper sequence: AT1G26810.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: AC206332.3_FGT005 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------gtacaacacaatctgacata-gctatgtttgcaaatagactgatttctgattcatttaa----cgaagtttct-actcaaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
|| || | ||| || || ||| | | | | | || ||| | | ||||| || ||||||||||||||||| ||||| ||||||||||| ||||| ||||| || | || || | ||||| ||| | | || | || | | |
gtaaattcttattaaattcctccctagacaatcgatgcatattccgttggatttatgttcatagaaaaatagaagaagagaccggcttatgtaccatttgcgatatttttttactgtatcaccatcaacatatgtaaatgccaacatttctgacatgttctccagGAATGGCCTGAAGATAAATACCCACCATGGGCTCATGGACCAGGATATGTAGTTTCACAAGACATTGCAAGGACAATCAACAATTGGTATAAGGCAAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcaaatagactgatttctgattcatttaacgaagtttctactcaaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
atttaac putative branch site (score: 3)
tttctactc putative PPT
attcatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaacacaatctgacatagctatgtttgcaaatagactgatttctgattcatttaacgaagtttctactcaaaaaacagGAATGGCCTGAAGAGAAATATCCACCATGGGCGCATGGTCCAGGCTACATTGTATCTCGTGACATAGCAGAATCGGTTGGTAAGCTTTTCAAAGAAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA