Sequence
atgc intronic sequence ATGC exonic sequencegttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54440.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------gttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcat-ataatggc----------agATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT-
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gtagactacctttctgaaacccctcatgaatttccttctatttccatgttatacatccactttttgtc--gatggctctactctcgctgatcatttccatcaaatgtacctgattatgccttctttgtttagGTATGCTAGAGAAGATACACATTATCTGCTTTACATATATGATTTGATGAGACTCAGACTGGTGAAAGAGTCTTCAGATGA-AAATGATCTTCTTTTAGAG
upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 6
---------------------------------gttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcatataatg-----gcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT-
|| || || ||| || || || | | || | || ||| | | || | | || || ||||| |||| ||| |||||||||||||||||||| ||||| ||||| || ||||| | ||| | || |||| | | | | || | |||| |||
gtgtttaacctatagaccctatctttcatttattttggtttagtct-tgcctcgtttttgtcctacatgttttac--tatttcatccagttttacccacttgcaaataactcctgtacagGTATGCTAGAGAAGATACACACTATCTGTTGTATATGTATGACTTGATGAGGTTGAGACTGCAAAAGGAGTCGACATCTGACAA-TGATCTTCTTCTAGAG
upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
--------------------gttagtatattctctgtctagtctctctcatgatt----gctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT-
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tcttttttattgtgtttggtgttgg-atattttttgtttgcttcttttctttatttctgacttgccatcagttatatataagtggc---tttacttctgcc--cagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTCAACATTTGA-AAATGATCTTCTTCTAGAG
upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
-----gttagtatattctctgtctagtctctctcatgattgct-ttgcattggttgagttgagctaacacatttgca--tataatggcagATATGCTAG--AGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAA--TGGCAAAGGAAGATGAGC-AATCTGACTCTCCT--
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gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA
upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
---------------------gttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT
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aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacacccta-attactgtaatctattgaatta--ttattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCAMapped 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|163975171|gb|ES008739.1|ES008739EST: GGAGAATAAGACCCCTTCCAGATGTAATGAAAAG ATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATG
genomic: GGAGAATAAGACCCCTTCCAGATGTAATGAAAAGgttagtatat ... ataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgattgctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT
agctaac putative branch site (score: 2)
atataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG