Sequence
atgc intronic sequence ATGC exonic sequenceTGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatttcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.5 |
intron # | 20 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GRMZM2G443953_T01 (Zea mays), 5'ss of exon 21
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatttcttacatgtggaacatatattcccgcaactaattacg-----tctatgctgatattaatatggttacag-----
||||| | | | ||||| | ||||||||||||||| ||||| ||||||||||| ||||| || || | ||||| || || || ||||||| || ||||| | | | | ||| | ||| | | | || || || | || | |||| ||| | | || | |
TGGCATCCATGTCTAAAGAACTAGGAAAGAACAATGTTGCTTTCCTTTGCTTGTTTATGTTAGGCAAATTGGAAGAATGTCTTCAATTGTTGGTTGATAGgtaggct-tctgcaattgaatgcatcttgccc-tactcagtaacatcttgtatcggacattgtatgttgacaattggtcctttgctgtacag
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 20
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtaca--ttgtttactatttcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag
||||| | | || ||||| ||||||||||||||||| ||||| ||||| || |||||| | || | | ||||| || || || || | | |||||||| | | | | ||| ||| | ||| | | | | || | || |
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctgggcaagattgccatacttaaccttaattttcttctttctagtttttgactctatcccttgtacag------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 20
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgttta-------ctatttcttacatgtggaacatatattcccgcaactaattacg--tctatgctgatattaatatggttacag--------------------
| ||| ||||| || |||||||| || |||||||| || || |||||||| || ||||||||| || ||||||||||||| || |||||||| |||||||| || | | || ||| | | || | | |||| | || || || | || ||| ||
TTGCAATCCTTGCCAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgtaattttctaaagttgggctgttttccttcctgacattactgatagggaggattgattagaaatttagaatgcagtttacat--ttatagctgaagtatgccttttgcag
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 20
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatt----tcttacatgtggaacatatattcccgcaactaattacgtcta-tgctgatattaatatggttacag--------------
| ||| ||||| || |||||||| || |||||||| || || |||||||| || ||||||||| || ||||||||||||| || |||||||| |||||||| || | || || |||| | | | |||| | | | ||| | | ||| | || ||| ||| ||
TTGCAATCCTTGCTAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgta-atcttctaaagttgtgctcttccctttatgacattactgatagggaaggattgattagaatgcagttacatttatagttgaagtatgccttttgcag
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 20
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatt----tcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag------------------------
| ||| | ||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||| || | || |||||||| || || ||||| |||||||| | | |||| || |||| || |||| | | | | | | | |||| ||| ||| |
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattat-tctactgttgtgatcttttattaatgacat-cactgtacagagagagaaagagagggttgattagaatgcagtttgatgtagctgagttatgcttttggcag
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 9
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatt----tcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag------------------------------
| ||| | ||||| ||||||||||| ||||| ||||| || || |||||||| |||||||||||| || | || |||||||| || || ||||| |||||||| | ||||| || | || || | || | | | || | | | | || | | |||
TTGCAACTCTTGCTAAAGAGCAAGGGAAGAATAATGTTGCATTCCTTTGCTTATTCATGTTGGGTAAACTTGAGGACTGCCTTCAACTTTTGGTAGAAAGgtattat-tttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtagctgagttatgcttttggcag
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 24
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtt--tactatttcttacatgtgga-acatatattcccgcaactaatt-acgtctatgctgatattaa-----tatggttacag
| ||| | ||||| ||||| || || |||||||| || || || ||||| ||||||||||||||| || | ||||| || ||||| ||||||||||| ||||| |||||| | || | | ||||| | | | | ||| | | | || | || | | | ||||| | | | | || |||
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgta-attgttgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcagMapped 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|47831644|gb|CK121328.1|CK121328EST: TTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAG TAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAA
genomic: TTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtt ... atggttacagTAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGCAGCACTTGCAAAAGAGCAAGGAAAGAACAATGTCGCTTTTCTTTGCTTGTTCATGTTGGGTCAAGTAGAAGACTGCCTGCATCTGTTGGTGGAAAGgtacattgtttactatttcttacatgtggaacatatattcccgcaactaattacgtctatgctgatattaatatggttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA