Sequence
atgc intronic sequence ATGC exonic sequence...ataaaaatagaaaataagaataaaaactattttctcaaattaaaccatctcttaacctttcactatcaagcctgattcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
Basic information
species | Glycine max |
transcript | GLYMA16G24610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15830.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------ataaaaatagaaaataa----gaataaaaactatttt--------ctcaaattaaaccatctctt--------aacctttcactatcaagcctgat--tcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
||| || ||||| || | || | | ||||| || | | ||| | | || | | || | | | | | || | | | ||| |||||| || |||||| || || | ||| | ||||||||||| ||||| ||||| |||||||||||| |||||||||| || ||||||||
gtatgtagcagagataagctctatcagaaccacacaaaagaatatcacattcggaaatagaaggagaaatgaactgtgtattattattatttctgtatgagcttagagaaaagaaccgctcctaggatgagctcaacagtgccgtgttttgtgactgaatttgcactcaaacctgcagGTTGGTGGCCCGTACTGGGATGTGCCACTTGGCCGGAGGGACTCACTGGGTGCCAGCATCCAGGGCTCCAACAACGACATCCCAGCTCCCAACAACACCC
upper sequence: GLYMA16G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G66390.1 (Arabidopsis thaliana), 3'ss of exon 2
ataaaaatagaaaataagaataaaaactattttctcaaattaaaccatctcttaacctttcactatcaagcctgattcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
||| ||| || ||| | | || | || | ||| | | | | | || | | || |||||| |||||||| |||||||||||||| |||| ||||| ||| | ||| |||||| | ||||| ||||||||| |||| || || ||||||||||| |
-------------------gtaagtact--catcacaattcactacacacaaaattagttgattatta----tcaataatttgacaaatgaaata-acagACGGGTGGACCGAGCTGGGAAGTACCTCTAGGAAGAAGAGACGCGAGAGGAGCAAGCTTGAGTGGTTCCAACAACGACATTCCTGCTCCAAACAACACTT
upper sequence: GLYMA16G24610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g02570.t01 (Vitis vinifera), 3'ss of exon 2
------ataaaaatagaaaataagaataaaaactatt-ttctcaaattaaaccatctcttaacctttcactatcaagcctgattcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
|| | || | | | | | | || |||| | | || || | |||| | | || | |||| | | |||| || |||||||||| || || |||||||| || || | || ||||||||||| |||||| ||| | ||||| |||||||||||||| || || ||||||||||| |
gtaagtattattatcagttgtcacatttttcagtcttgttcttgacatggcacagctacca-tctttagccagcatgg-tgatatttacttctttttgagtgtacagACTGGGGGGCCTAGCTGGGAGGTGCCACTGGGGAGAAGGGACTCCAGAGGTGCCAGCTTGAGTGGTTCCAACAACAACATTCCTGCTCCAAACAACACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctcttaacctttcactatcaagcctgattcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
cctgattcactttccc CT-rich tract
ttttttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaaaatagaaaataagaataaaaactattttctcaaattaaaccatctcttaacctttcactatcaagcctgattcactttcccttttttgtatacagACTGGTGGACCAAGCTGGGAAGTACCCTTAGGCAGAAGGGACTCACTAGGTGCAAGCATAAGTGGCTCCAACAACAACATCCCAGCCCCAAACAACACAT
- aaaaata
- - - - - aaaataa
- - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcctga