Sequence
atgc intronic sequence ATGC exonic sequence...gaggcttatcttgttgcttatgatactgtgtgtgttcatgaaaaatcctatcccgttctgtgatttccttatggtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 2
gaggcttatcttgttgcttatgata-ctgtg---tgtgttcatgaaaaatcctatcccgttctgtgatttcct--tatggtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
|| | || || || |||| | || || |||| | || | | || | | || | | | ||| ||| | || ||||||||||| ||||| ||||| |||||| | | ||||| ||||| ||||| ||||| |||||| |||||||||||||| | || || ||||| || |
----tttctatttttactgatgaaagctttggactgtgattgtgtgtcctttgtcttcattgaatagtatctaagtgcaatctccactgt-catttggtat-ccagGTGACATCCATGGTCAATACAGTGATCTTCTAAGGCTTTTTGAATATGGAGGCTTTCCTCCTGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G07080.1 (Glycine max), 3'ss of exon 1
gaggcttatcttgttgcttatgatactgtgtgtgttcatgaaaaatcctatcccgttctgtgatttccttatg-gtttgtggtgtacatgtcttaaac----cagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
|| | |||||| | | ||| || || | | | || || ||| |||| | | ||| | | | | |||| |||||||||| |||||||| || ||||||||||| ||||||||||| ||||| || || ||||||| |||||||||||| ||| | ||||||||||||||| |
----ctgttgttgttgttgaattgtttgttagtttttctatttagcattg-cctgtagtgttattttatggcatggttgagatctctctctcttcgctttttcagGTGACATTCATGGGCAGTACAGTGATTTGTTAAGGCTATTTGAATATGGGGGTTTGCCTCCTACTGCCAATTATCTCTTTTTGGGGGACTATGTGGACCG
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G41890.1 (Glycine max), 3'ss of exon 1
gaggcttatcttgttgcttatgatactgtgtgtgttcatgaaaaatcctatcccgttctgtgatttccttatg-gtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
| || | ||||| | | ||| | || | || | | || ||| |||| | | ||| | | | | | | |||||||||| |||||||| || ||||||||||| ||||||||||||||||| || || ||||||| ||| |||||||| ||| | |||||||| |||||| |
tattgttttaatgttgttgaattgtttgttagcttttctatttaacattggct-gtagtgttattttatggcatggttgagatctctctttgctttttcagGTGACATTCATGGGCAGTACAGTGATTTGTTAAGGCTATTTGAGTATGGGGGTTTGCCTCCTACTGCGAATTATCTCTTTTTGGGGGACTACGTGGACCG
upper sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 3'ss of exon 1
---gaggcttatcttgttgcttatgatactgtgtgtgttcatgaaaaatcctatcccgttctgtgatttccttatggtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
||| | | | | ||| ||| | | || ||| | | |||| | | | ||| || || | | | | | | ||||||| || ||||||||||| ||||| ||||| ||||| ||||| || || || || |||||| |||||||||||||| | |||||||||||||| |
atgtaggatggaaatttgtcatat-atattttttgagtttcttgtgataattatctggattgat--ttttctgatcttgtaaatttgcccttggtggtttcagGTGATATTCATGGGCAATACAGTGACTTGTTAAGGCTTTTTGAATACGGGGGGTTTCCTCCTCACACCAATTATCTATTTTTAGGGGACTATGTGGATCGMapped 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|125290639|gb|EL304724.1|EL304724EST: AGGCTCCCATCAAAATCTGTG GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTAATGGT
genomic: AGGCTCCCATCAAAATCTGTGgtatcttccc ... cttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTA-TGGT
EST:
gi|19876690|gb|AU237521.1|AU237521EST: CCTTCAGCAACCCAATTTACTTGAGCTTGAGGCTCCCATCAAAATCTGTG GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTG
genomic: CCTTCAGCAACCCAATTTACTTGAGCTTGAGGCTCCCATCAAAATCTGTGgtatcttccc ... cttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctatcccgttctgtgatttccttatggtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
tcttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaggcttatcttgttgcttatgatactgtgtgtgttcatgaaaaatcctatcccgttctgtgatttccttatggtttgtggtgtacatgtcttaaaccagGTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAGTGCCAATTATCTATTTCTTGGGGACTATGTGGACAG
- - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgt