Sequence
atgc intronic sequence ATGC exonic sequenceAAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42270.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatactactg--atcctagct----actt---cttgtgttattattgtgttgaccactcactgttcaat-----aaaattgtaatttgcag
|||||||| || ||||||||| | ||||||||||||||||| ||||| ||||| || |||||||| || || ||||||| |||||||| |||||||||||| | || | || || || |||| || |||| | |||| | | || || || || || |||||||||
AAGGATGAGATCTCTGATGCTTTGGAGAGGATCATTGCTGGGCCTGAGAAGAAAAATGCTGTTGTTTCAGAAGAGAAGAGGAGACTTGTGGCTTACCATGgt-aaatcttgtcaccatattaacttgtgacttgagctgaaattatcctggtgtgcagaggttcctaatccatttttgaacttttcaatttgcag
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G126361_T03 (Zea mays), 5'ss of exon 3
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatactactgatcctagct----acttcttgtgttattattgtgttgaccactca----------ctgttcaataaaattgtaatttgcag
|||||||| || ||||||||||||||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||||| || || || |||||||||||| | || | | || | || || | | | | | |||| ||||| || ||| |||||| ||
AAGGATGAGATCTCTGATGCTCTTGAGAGAATCATTGCTGGCCCTGAGAAGAAAAATGCTGTTGTTTCCGAGGAGAAGAAGAGGCTCGTCGCTTACCATGgt-aaatgttgtcaaatttatattataaccataagtttgactcccgcttacggggctcaggttcctaatctgttgttgaactttggaatttgtag
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgt-tagatactactgat--cctagctacttcttgtgttattattgtgttgaccactca---ctgttcaataaaattgtaatttgcag
|| ||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| || ||||||||||| || |||||||| | | | || || || |||||| | || | | || || | | ||||| | | | ||| | ||| | || | || | |||| |||
AAAGATGAGATATCTGATGCGCTTGAAAGGATCATAGCTGGACCTGAGAAGAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcag
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgt-tagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcag-------------
|| ||||| ||||||||||| ||||| |||||||| |||||||| || ||||| || ||||| ||||| || |||||||| | | | || || || |||||| | || | | | | | | ||| | | |||| | || | | || | | ||| |
AAAGATGAGATATCTGATGCGCTTGAAAGGATCATAGCTGGACCCGAGAAGAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcag
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgt---tagatactactgatcctagct--------acttcttgtg-ttattattgtgttgacc------actcactgttcaataaaattgtaatttgcag
|||||||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| ||||| || |||||||| | | | ||||| || |||||| || | | | | |||| ||| || || ||||||| ||| |||| | | | | | |||||||||
AAGGATGAGATATCTGATGCCCTGGAGAGGATAATTGCTGGGCCAGAGAAGAAAAATGCTGTGGTCTCAGACGAGAAGAAGAAATTAGTTGCCTATCATGgtacataaaagagaacaacacaagctttgtacaggtctctgatgcttgttattgttttgggtgttttaactctttatgtgtttgcacttgaatttgcag
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ37923 (Selaginella moellendorffii), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcag
|| ||||| || ||||||||||| || | ||||| ||||||||||| |||||||| ||||| || || ||||||| ||| | || ||||||||||| ||| || | | || |||| | || | | | || | | | || | | | |
AAAGATGAGATCTCTGATGCTCTGGAACGAATCATCGCTGGACCTGAGAAGAAGAATGCTGTGGTTTCGGAGGAGAGGAAGAAGCTGGTTGCTTACCACGgtaag------caaactct---cacttttagtttcgtcggggacttactcg---agtttttgttggagtag----------
upper sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ31931 (Selaginella moellendorffii), 5'ss of exon 2
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttag-atactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcag
|| ||||| || ||||||||||| || | ||||| ||||||||||| |||||||| ||||| || || ||||||| ||| | || ||||||||||| ||| || | ||| || ||| | | || || | | | ||| |||| ||| |
AAAGATGAGATCTCTGATGCTCTGGAACGAATCATCGCTGGACCTGAGAAGAAGAATGCTGTGGTTTCGGAGGAGAGGAAGAAGCTGGTTGCTTACCACGgtaagcaaactctcactcttagtttcgtcgggtacttaactcgagttt--------ttgttgaatgtag-------------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|125209827|gb|EL224781.1|EL224781EST: GAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATG AGGCTGGGCATGCTTTAGTTGGTGCACTTATGCC
genomic: GAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatact ... taatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGGATGAAATATCTGATGCTCTTGAGAGGATCATTGCTGGACCTGAAAAGAAGAACGCTGTTGTCTCTGAGGAGAAGAAAAGACTTGTTGCTTACCATGgttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA