Sequence
atgc intronic sequence ATGC exonic sequenceGCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50950.3 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G02040.2 (Glycine max), 5'ss of exon 2
GCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttag-----
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TCAAAGATCGTTGCAGAACTTCGACATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCTTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattcatatatatcttc----acttcttctacttgcactatcctctttcaaaaattatcaattgttgttttgatgcag
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 2
GCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGg------tttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttag-----------------------------------------------
|| |||||| | ||||||||||| || ||||| |||||| || ||||||||||| ||| | || || ||||| |||||||||||||| ||||| |||| || | | | ||| || | | | |||| | | ||| | | || | || | ||||
TCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattcattttttcacttcttctacttccactgcaacattttctatgtttaggtattttggtcgtagatttcgattttgattattattccatcctctttcaattgatcaatggttgttttgatgcag
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G01930.2 (Glycine max), 5'ss of exon 2
GCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtt----tttgcagtaaagtctcttatgtaaattatcc-----tttttttttttttttaggttcgtgattttacgatgatgttttag-------------
|| |||||| | ||||||||||| || ||||| |||||| || ||||||||||| ||| | || || ||||| |||||||||||||| ||||| ||||| || | |||| || | || | | | || | | | | | || | |
TCAAAGATCGTTGCAGAACTTCGATATCGGTGGGCCCCGCGAACGCATGCCCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattcattttttcacttcttctgcactgcatgcagccatgcaccatcccttcttagctacttgctgcacagttaccccaggactgtggtaactac
upper sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcagtaaagtctcttatgtaaatt-atcctttttttttttttttaggttcgtgattttacgatgatgttttag-----------------------
|| ||||| | ||||| || || ||||||||||| || || | |||||| ||||||||| | ||||||||||| || | || ||||||||||| |||||| || |||| | || | || | | | | | | || | | |||| | | ||||| |
TCAAAGATCATTGCAGAATTTTGATATTGGTGGTGAGCGTGAACAAATGCCTGAACCAATCATTCGAGCTTTTGGCATCCTTAAAAAATGTGCTGCAAAGgttgtttcagttgtacatttttccttttcagattcatactgctatgacattggctgataatttgataac--tgtttaaagaatttgggttctgtttagtgggMapped 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|116443356|gb|EG485948.1|EG485948EST: CCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAG GTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAA
genomic: CCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcag ... gatgttttagGTTAACATGGAGTATGGTCTTGATCCAATGATTGGGGAAGCCATAATGGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAGAGATCGCTTCAGAACTTCGAGATTGGTGGTGACCGCGAGCGAATGCCCGAACCAATCGTCCGAGCTTTTGGTGTCTTGAAGAAATGTGCTGCCAAGgtttttgcagtaaagtctcttatgtaaattatcctttttttttttttttaggttcgtgattttacgatgatgttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC