Sequence
atgc intronic sequence ATGC exonic sequencegttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 3
-----------gttcttaaactctc-ttcagaacgtttccaaaatgttc-tgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
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gttattttcctttgcatatcctctcatttgagactttggtgagaaataggcatatgcatatgtttattctgatgtggcttgttttttttcatgga---tgtagACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 4
---------------------gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
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gttattttcctttatgtatcatttcatgaaggactttcatgagaattagttatcaataaatatatgtttattctaatatggcctattttgtttgctttatgga---tgcagACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTG
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 5
------gttcttaaactctcttcagaacgttt--ccaaaatgttctgtgtttttttttgaaaccat--ctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
||| | | | ||| ||||||| | ||| ||| | |||| | | |||| | ||||| ||||| ||||| || ||||| ||||| || |||||||| ||||| ||||| || ||||||||||| || |||
agaaggaaaaaaaaaaaagttatggtatctttggtttgaatgttcaaccatatttgaactaactgtggcttttgtttctggttcttgtgttgttgaacagACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATT
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36429 (Selaginella moellendorffii), 3'ss of exon 3
--gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttt-tgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
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gtttttctctcttttctttggtttttcctctacttgtcctttcttttctttgcgaagttggattttcatgtttttgttt------cttcacagACCATGGCTTGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTT
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
---gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttt-tttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
|| || ||| | || | | || | | ||| | |||| ||| | || | || | ||| | || | || ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| || ||
gtttttttttcacttttttttgttctttcttttatttttcatttttttgtttcttttacaaagttggatttttatttttttggtttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
||| || | | | |||| | | | | ||||||| || ||| | ||||| || || ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| || ||
gtttttttctttttcttttgttctttc-----tttcttttctttttttgcaaagttggattttcattttttttgttt-----cttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 3
--gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaa-ccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
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gtttttctctcttttctttggtttttcctctacttgtcctttcttttctttgggaagttggattttcatgtttttgttt------cttcacagACCATGGCATGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTTMapped 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|116386886|gb|EG429478.1|EG429478EST: TTGGGATTCATACTGATGTTCCAGCTCCAGATATGGGCACTGGTCCTCAG ACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCT
genomic: TTGGGATTCATACTGATGTTCCAGCTCCAGATATGGGCACTGGTCCTCAGgttcttaaac ... gaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
tttttttttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttaaactctcttcagaacgtttccaaaatgttctgtgtttttttttgaaaccatctttcaactttttcccttggtggaatttgcagACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG