Sequence
atgc intronic sequence ATGC exonic sequence...ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33950.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagt-caaatgc-atcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
||| | | | | || | | | | || || | ||| | | | || ||| | | ||| | ||| || | | | || |||| ||||| ||||| ||||| || || || || || ||||||||||| ||||||||||| || ||||| || || || |||||||||||||| || |
gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgag-gcatcagtgcgattgctgactaaatatttgtttctcaacaaagATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 6
--ttggtgaagaaagctattaagagtctgatttgtaa-actgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttt---tcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
| | | || || |||| | |||||||| | ||| | || ||| | ||| || || | || | | ||| ||| ||||| ||||| ||||| || ||||| ||||| ||| | ||||| |||||||||||||| ||||| || || || ||||| ||| | ||||| |
tgtcccttctttttctttaaaacagaagtatttccattactgataaccgcttagtgtagg---aatc---ctggctcatactgatacattatttatactgaaacagACTGCTGATGTATGGTCCTGTGGTGTGACTCTATATGTTATGGTAGTTGGTGCATATCCTTTCGAGGATCCAGAAGAGCCTAAGAACTTCCGTAAAACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 6
ttggtgaagaaagctattaagagt-ctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttt-----tcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
| || | | || || | ||| | || | | || | || || || | | | || | | || | |||||||| | || |||| | |||||||| |||||||||||||| || | ||||||||| ||||||| ||||||||||| || ||||| |||||||| || |||||| | || || |
gtagtagaatgaaaggttgtgattactgttatgcatgc--atggt-ctagaattcagctagcttt--ttatctgt-tgctaatgtttacactcaattatgactcagATAGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 6
ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagtca--aatgcatcctaatgttcttcttttttt--------tcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
| | | || ||||||| | || || ||| |||| | ||| | | ||||| | || || | || || | |||| |||||||||| |||||||||||||| || | ||||||||| |||| || ||||||||||| || ||||| |||||||| || |||||| |||| || |
---------attaatgtgaaagcactgattt-caggctagctatgctttttttttccctttcttatttactaatgccttgtattgatgtttccattctactatgactcagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 6
ttggtgaagaaagctatta-agagtctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
| | | | | || | | | | | | | || ||| || || | ||| | || || | |||| || | || ||| |||||||||| |||||||||||||| || | ||||||||| |||| || ||||||||||| || ||||| |||||||| || |||||| |||| || |
tagatattagatgttaatgcaaaagattcctggctagctatgcatttttttcttatttagtaatgccttgtattgatgtttccattctactatgatt-cagATTGCAGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 6
ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgtt-----cttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
|||| | | ||| | | | | || | | | | | || | || ||| || | | || || ||||| | || | |||| |||||||||| |||||||| ||||| || | ||||||||| |||| || ||||||||||| || ||||| |||||||| || |||||| | || || |
--aatgaa--aggttatgattactattatgcatgcatggtctagaactcagctagctttttatttgttactt-tatactgatgttgacacccaattatgactcagATTGCAGATGTGTGGTCTTGCGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 6
ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagt-tttggttgaattagtcaaatgc-atcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
||| || || | || |||| | || || | ||| || | | | ||| | | || | || || || || ||||||| |||||||||| |||||||||||||| || | ||||| |||||||| || || || || || || || || |||||||| ||||| ||| || || |
-tggaaaatgtagtttgtatgagtataatg-gttatatgagaacaccaaaatatttagacttactaatgttttgttgctctgatatttgatcacattttcagATTGCAGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------ttggtgaagaaagctattaagagtctgatttgtaaac-----tgataattcttgagttttggttgaa------ttagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
|| || | || ||||||| | | || || | || | | ||| || | || |||| | | || | | | | ||| |||||||||| |||||||| || ||||| |||| || ||| |||||||||||||||||||||| ||||| || || |||| ||||||||||||||| |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgccgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------ttggtgaagaa-------agctattaagagtctgatttgtaaactgataattcttg--agttttggttgaattagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
||||| || || | | || | ||| || | | ||| | || | || |||| || | || | | ||| |||| ||||||||||| || || || ||| |||| || ||| |||| ||||| ||||| || || |||||||| || |||| ||||||||| |||||||
gtgagttcgtcggacgataacttagttgtattggtatggagtagtcccggcgttgtattgttagtttttccaagtagacgctgttgtcgatagtgtcggtatcggtcagctgagaagacagaaatgctttgatatgcagATTGCCGATGTTTGGTCGTGCGGTGTGACTTTGTACGTGATGTTGGTCGGAGCGTATCCCTTTGAGGATCCCGAAGATCCAAGGAATTTCAGAAAAACTA
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------ttggtgaagaaagctattaagagtctgatttgtaaa------ctgataattcttgagttttggt-tgaatta--gtcaaatgcatcctaatgt-------------tcttctttttt-----ttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
|| ||| | ||| | | | || | | || | | || | || || || | | || || || ||| | || | | ||| || | ||| |||| ||||| ||||| || || || || |||| |||||| |||| |||||||| || ||||| |||||| | || |||| ||||||||||||||| |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCAMapped 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|164175149|gb|EL997597.1|EL997597EST: ACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG GTTGCAGATGTTTG
genomic: ACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAGgtactccatt ... tttttttcagGTTGCAGATGTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
tcctaat putative branch site (score: 2)
tcctaatgttcttctt CT-rich tract
ttcttctttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggtgaagaaagctattaagagtctgatttgtaaactgataattcttgagttttggttgaattagtcaaatgcatcctaatgttcttcttttttttcagGTTGCAGATGTTTGGTCTTGTGGGGTTACTCTGTATGTCATGCTGGTTGGAGCATATCCTTTCGAAGATCCCGAGGAACCAAAGAATTTCAGGAAAACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - -gaagaaa
- - - - - - - - - - - - - gatttgt
- - - - - - - - - - - - - - - - -aaactga
- - - - - - - - - - - - - - - - - - - - - - - - - gttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcctaa