Sequence
atgc intronic sequence ATGC exonic sequence...taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
-----taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagA--AAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
| ||| | || | | | | | | | || | | | | | | | || | | | || |||| || || | |||||||||||||||| ||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| ||| | |||
taatctggtgtggatttt-tgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG------
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 1
----------taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagA--AAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
| ||| | || | | | | | | | || | | | | | | | || | | | || |||| || || | |||||||||||||||| ||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| |||
ttcagtaatctggtgtggatttt-tgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtagGTAAGGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCC-----------
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 1
---------------------taatgttgcttgtgtaacatgattagggttgaaatcta-tgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
| | ||| | || || | | | ||| |||| | ||| | ||| ||| || | |||| | | || |||||||||||||||| ||||| | | ||||| |||||||||||||| ||||||||||| ||||| |||||
tggagctggcggcagctcgttgattcttgttcccgtggtgtgctcgttgctcgtctctgctgatgccgtcactgttgcgtt--gttgatgtgtacag-gtaagAAGGAGAGAAAGAGGGCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCA-------------------
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34760.3 (Glycine max), 3'ss of exon 2
---taatgttgcttgtgtaacatg----attagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgttt---gttgcttagAAAAATG---AAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
| |||| || | | || | || | | | |||| ||| | | | || | || || || | | || || ||| | || | || ||| ||||| ||||| |||||||| | | |||||| || |||||||||||||| ||||| ||||||||||| || ||||| ||
gttgattgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggt-tgactttaatgtgtaagGTAAGCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCA------------
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34760.4 (Glycine max), 3'ss of exon 1
taatgttgcttgtgtaacatg----attagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgttt---gttgcttagAAAAATG---AAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
|||| || | | || | || | | | |||| ||| | | | || | || || || | | || || ||| | || | || ||| ||||| ||||| |||||||| | | |||||| || |||||||||||||| ||||| ||||||||||| || ||||| || ||||
--ttgttagttatctgctattttacactatcttgtgcttatcctattaccttattacataatctaacctgttgtcgtggt-tgactttaatgtgtaaggtaagCCAAAACCATGGTTAAGCATAACAATGTTATCCCAAACGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACTTGGTTCAATCAGCCAGCACGGAA-------
upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
--taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgta---acatttgtgtttgttgcttagAAA-AATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
| | | | | || |||| | | | | | || | | ||| | | | || | | ||| | | || | | ||||| ||||| ||| | || | ||||| || || ||||||||||||||||| |||||||||||||| ||||| | ||
tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA------Mapped 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|125250174|gb|EL264259.1|EL264259EST: GGAGAAGCCTTCACTTTTCGTCCAAGCCGCT AAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAG
genomic: GGAGAAGCCTTCACTTTTCGTCCAAGCCGCTgtgagtatcc ... tgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAG
EST:
gi|124749100|gb|EH839230.1|EH839230EST: TCTGGAGAAGCCTTCACTTTTCGTCCAAGCCGCT AAAAATGAAGCACAACAACGTTATCCCGAGCTCAGACTTTCG
genomic: TCTGGAGAAGCCTTCACTTTTCGTCCAAGCCGCTgtgagtatcc ... tgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
ttgtaac putative branch site (score: 2)
tttagtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgtaacatttgtgtttgttgcttagAAAAATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - -aacatga
- - - - - - - - - - - - - - -tgaaatc