Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgtactttctccaaagctatcatgtagtgtctttaaggaaagggtggttgaccaacattattagtcgatagattttatcttcccagtttattgttctgttgctaaataagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63120.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G02590.1 (Glycine max), 3'ss of exon 5
gtatgtttgtactttctccaaagctatcatgtagtgtctttaaggaaagggtggttgaccaacattattagtcgatagattttatcttcccagtttattgttctgttgctaaataagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
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---------------------------------------------------------agaactattgtcactggatatgtcctatgttt---gtgtgtgattttcatactgattttg---tataagagactcggttagatacat----ttgtgatttgaaatac-cagATTCGACCAGATAGGCAAACACTATTATGGAGTGCTACATGGCCAAGGGAGGTTGAAACTCTGGCAAGGCAGTTTCTGCGCAACCCATACAAG
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 5
gtatgtttgtactttctccaaagctatcatgtagtgtctttaaggaaagggtggttgaccaacattattagtcgatagattttatcttcccagtttattgttctgttgctaaataagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
|| ||| ||| ||| || | ||| || || | | | || | || | || |||| || | | ||||| ||||| ||||| |||||| | | |||||||| ||||||||| | || ||||||||||| || ||||||||||| | | ||||| |||
----------------------------------------------------------------ttcttaa--gatgagaactattctcactagatat-gtcctatgtgtgtgggtgtgtgattttaatacattttgtatagttacatttgtgatttgaaatac-cagATTCGACCAGATAGGCAAACATTATTATGGAGTGCTACATGGCCAAGGGATGTTGAAACTCTGGCAAGGCAGTTTCTGCACAACCCATACAAG
upper sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtttgtactttctccaaagctatcatgtagtgtctttaaggaaagggtggttgaccaacattattagtcgatagattttatcttcccagtttattgttctgttgctaaataagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
| | | | | | | | | || || | || || | |||| | | | | |||| | |||| |||| | || | |||||||||||| |||||||| ||| | |||||||| ||||||||| | ||||| |||||||| || |||||||| |||| ||||||| |||
---------------------------------------------------------atcttc-tcaagaactgggtgtactgatgtttttaacataaaaatccttaaaaaaatgatgagctttggagctta-atacaga---tgag------ttctgttaattacagATCCGACCAGATAGACAGACATTATACTGGAGTGCCACATGGCCAAGGGAGGTGGAAACTCTAGCGAGGCAGTTCTTACGTAATCCATACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
ttgttccttatttttc CT-rich tract
ttatttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgtactttctccaaagctatcatgtagtgtctttaaggaaagggtggttgaccaacattattagtcgatagattttatcttcccagtttattgttctgttgctaaataagaaccatcacggcttttgttcagaacttgagattgttccttatttttcacagATCCGACCTGATAGACAAACACTTCTTTGGAGTGCAACATGGCCACGAGAGGTTGAAACTCTTGCCAGGCAGTTTCTACGAGATCCATATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC