Sequence
atgc intronic sequence ATGC exonic sequencegtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19450.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 9
------------------------gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaat-ctcatacgaatttg-atatttttagtttcttag--agtcggtgatgtaatttcag--ttactgaacgcaaatctcttgtc-caaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
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gtaatttccattttctacttattcataatcaagaaaatggtcactattagacta--taatatattc-aaaatcaatttatttctgaatgcatacatttccttgcatgatccaagcttgtgaacaaataatttctctaacaccagacttacagtttaaacattgataattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 9
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
|| || | || | |||| ||| | | | || || || | | | | || | || ||| || | | | | ||| || |||| || || | || ||||| ||||| || || ||||||||||||||||| || ||||||||||| |||| || | |||
-------------------------------gttttggatc---agaatgggaaaaacataagttttaccataaccagag---ttcaacctttca---tc--tcatactgcttccgtgcatttttgttccttttctgtaca--gGTTGAATATTCTTGCTGAGCTCCTCTGTTTTGGTGATCGTGAATTCTACAAGGACTGGTGGAATGCCAAAACAGTTGAAGAG
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G130749_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------gtatgctgtgatcccatctc-tttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatat-ttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
||| | | || | || || || | | || | | || | || |||| | || || | ||||| |||| | | || || ||||| | |||| | || || | | | |||||||||||| | || ||| |||| | || || || || |||||||||||||| |||||||||||||| | | | ||
gtagtaaattatattttctatctattcattcaaattcaaatacatgatcgatcctgatattattctaatatcagtcatcgatgcttcttctccgaacatgcatgctctcggagaaaattatttccttttatgctctttcaaat--ttgcatatttgcagtttc-gaacttatat-tcatctatacagGTTAAACATACTTGCTGAGATTCTTCGATTTGGTGACCGAGAATTCTACAAAGACTGGTGGAATGCAAAGACAATTGATGAG
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
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-------------------------------ttgtctcatttgtagatattagaaaaggttcacct---------ttgattttttaagatttagttaatatttgaggaagctt--atcattgga-gtgactgtcgtaat-gtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
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------------------------------ttgtctcatttctagatattagaaaatgttcacctttgtttt--tttaagatttagttcatatttgaggcagct-tatcattggagtgactg--ttccaatgt---------agGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
upper sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g01930.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcgg--tgatgtaatttcagttactga-acgcaaatctcttgtc-caaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
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------------------------------------------taaaaatataaacagagtttac------caattctattatctttcatttgtctgaatcatattactaagacatatcatacttagatgcagtgttgcaattatatagGTTAAATATACTTGCTGAGCTTCTTCGTTTTGGGGACCGTGAGTTCTATAAAGATTGGTGGAATGCAAAAACAGTTGAGGAGMapped 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|124836035|gb|EH920474.1|EH920474EST: CCAAATTTATATGTGTGGCTCTGCATGTTCTACTGCTTCTTCCACCTTTG GTTAAACATATTGG
genomic: CCAAATTTATATGTGTGGCTCTGCATGTTCTACTGCTTCTTCCACCTTTGgtatgctgtg ... ttgtccaaagGTTAAACATATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
tctcttgtcc CT-rich tract
atgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT