Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcctttggacatccatagtcaaataagcctacaggtttataatgtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09980.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G19570.1 (Glycine max), 3'ss of exon 8
---gtaagtttcctttggacatccatagtcaaataagcctacaggtttataatgtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
||| | | | | | || | |||| | | | | || || | | || | | | | | || | | ||||||| ||| | ||||| || |||||| ||| || | ||| |||| ||||||||| | || |||||||||||||||||||||||||||||||| |||
gaaaaaagatacactcagttaaatatcttttaata--ttaagccttccttcaagtcaatgacatggtttttctcttcctttttattctcatcgcttcatcagGGAAAATAAAACAAAGATACTGGAATTTCTCCGTAACTCATGGGCTAATGATCGAAGAACTGAGTGGTCAATATGGATGGTGTACTCCAAGGTTGATATG
upper sequence: AT1G09980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G26570.1 (Glycine max), 3'ss of exon 8
gtaagtttcctttggacatccatagtcaaataagc-ctacaggtttata-atgtttgcgaagttatcttctgatc--attgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
|| | || | | | || | | | || |||| ||| || | | |||| | || || || | | ||| |||| |||||||| | ||||| || | |||| | | | ||| ||| |||| ||||||| ||| |||||||||||||||||||||||||| ||||| || |||
---tgtctgacatgacaaacaagagaggtgtccgtgtttcatagttatccatgcatgagtatatatcatgaaatttaatcagctacaatattcttgtttttagGGATAACAAAACAAAGATTCTAGAATTTTTGCATGATGCTTGGGCTAAGGATCGAAAAGCTGAATGGTCAATATGGATGGTGTACTCTAAGGTCGAGATG
upper sequence: AT1G09980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G05480.1 (Glycine max), 3'ss of exon 10
-gtaagtttcctttggacatccatagtcaaataagcctacaggtttataat-gtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
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agatgcactcagttaaatatcttttga-gcataatattaagcattccttctagtcaacgacatggtttttctcttcctttttattctcatcgcttcatcagGGAAAATAAAACAAACATACTGGAATTTCTCCGTAACTCATGGGCAAACGATCGAAGAACTGAGTGCTCAATATGGATGGTGTACTCCAAGGTTGATATG
upper sequence: AT1G09980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G08190.1 (Glycine max), 3'ss of exon 9
-gtaagtttcctttggacatccatagtcaaataagcctacaggtttataatgtttgcgaagt---tatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
| | | | | | || ||| | | | | ||| ||| |||| |||| ||| | | || |||| || || |||||| || | |||||||| |||||| ||| || | |||| | ||| | ||| | |||||||||||||||||||||||||| ||||||| ||||
aactgttatgttgtaggaaaagatgcacaattcaagcataacattttagctgtacattaagtcgatatcatctctttttcaaccttatcattttact---cagGGAAAACAAAACAAAAATACTGGAATTTCTACGTAAATCCTGGGAGATTGATAGGAGAACTGAATGGTCAATATGGATGGTGTACTCAAAGGTTGCAATG
upper sequence: AT1G09980.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0055g00430.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtttcctttggacatccatagtcaaataagcctaca-ggtttataatgtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
||| | | ||| | | ||||| | ||| | | || || || | || | || | | || ||||| ||| | | ||| || |||||| ||| ||| ||| | || ||||| ||||| |||||||||||||||||||| ||||| ||||| || |||
aaaagggagaaatagttgagcatgtggattttgcactacatgatttgtgcttatttttctgtgccattaattcaaatgctgatgttatactttgttccagGGCTAACAAAAAAAAGATACTGGAATTTCTGATTGATGCATGGGCGAATGATCGGAGAGCTGAATGGTCAATATGGATGGTATACTCTAAGGTCGAGATGMapped 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|86060117|gb|DR355874.1|DR355874EST: CTGTGCACCCAGCTCCATTATCTATGGAATACCTTTCTGACATTGCACCG GGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGA
genomic: CTGGGCACCCAGCTCCATTATCTATGGAATACCTTTCTGACATTGCACCGgtaagtttcc ... cccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataatgtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
cattgac putative branch site (score: 3)
ttgactttatttttcc CT-rich tract
attgactttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcctttggacatccatagtcaaataagcctacaggtttataatgtttgcgaagttatcttctgatcattgactttatttttccccttttcagGGATAATTACACAAAAATCTTGGAATATCTTCGCGATATCTGGACTAAAGATCGAAGAGCGGAATGGTCAATATGGATGGTGTACTCCAAGGTTGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA