Sequence
atgc intronic sequence ATGC exonic sequenceCACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg...
Basic information
species | Glycine max |
transcript | GLYMA04G37920.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg
| ||| | |||||| | |||||| | || || |||||||||||| |||| ||||| ||||| ||| ||||||||||| ||||| || ||||||||||| | | ||| | ||| ||| || | |||| | || || | || | || | | | | | ||
CTCACTTGATTCCTCCTGATACTCCCCGTTCAATCTTTGTTTACTTCAGAGGCCTGTTCTATGACAATGGGAATGACCCTGAGGGTGGGTATTATGCAAGgtaagaat-gtttgc-agaaccttgaaagatacatctcctgtgg-tacttggtcctgctttattgactctgttgaacttgttatacag------------
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg
| ||| | || || | ||||| | || || || || |||||||| ||||| || ||||| |||||||||||| || ||||| ||||||||||||| | | ||| ||| || | ||| || | || | | | | || || | | | | || || | | |
CTCACTTGATCCCCCCTGACACTCCACGTTCAATCTTCGTCTACTTCCGGGGACTATTCTATGACACTGGAAATGACCCCGAGGGTGGTTACTATGCAAGgttagcaatgttt-tta-aagtaacagatctgaattt----ttatccttctggttttgtcccatgtactcacttcagtgatgttatacag----------
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G023020_T01 (Zea mays), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcat-gtctggttaagaccactaacttg
| ||| | ||| | | | ||||| | || || || ||||||||||| ||||| |||||||| || |||||||| || || ||||||||||||||||| | || | | | || | || || | | ||| | || |||| | || | | | |
CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactgcttttcaagttt---gaacagatttgaatcttgtatgtttgatacctt-cattcacttcaatattgtcatacag-----------------
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgta-tgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttca-----tttatttttgcagcat--gtctgg---ttaagaccactaacttg-------------------------------------------------------------------------------------
||||| ||||||| ||||| ||||| | ||||| || ||||| ||| ||||| ||||||||||||| |||||||||||||| ||||| || ||||| ||||| | | || |||| | | || | | | | | | || | | || || |||| || || ||| || ||| ||||
CACACTTAATTCCCGAAAAAACTCCTCGATCCATCTTCGTTTATTTCAGAGGATTGTTTTATGATGTGGGAAATGACCCTGAGGGTGGTTATTATGCGAGgtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacag
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg--
| ||| | || || | | ||||| ||||| || ||||| |||||||||||| |||| |||||||| ||||||||||| |||||||| || |||||||||||| || | ||| | | | || | | ||||| || | | | ||||||| |||||| | | || |
CCCACTTGATCCCGCCAGACACTCCTAGGTCTATCTTTGTCTACTTCCGAGGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAGgtattcctcaca-atttttatatgttgacattggggtgtt-tagacatcgaagtgatatgaaatatttttaatgcatgtataaatcctttcaatgggagaga
upper sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 5'ss of exon 3
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgt---cttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg
| ||||||||||| || | || || ||||||| || ||||||||||| || ||||||||||||| ||||||||||||||||| ||||||||||||||||| | | | || || | | | || | || || |||| | | | | | || ||
CCCACCTAATTCCCCAAGAAACCCCTCGGTCCATCTTCGTTTACTTCCGTGGTTTGTTTTATGATGTGAATAATGACCCTGAAGGTGGTTACTATGCAAGgtatgtgggttagtgttttttttttcctttttcttttcctcttattgagaattgca--ttgaaatttgataccatgggcaattcaataataggggttaggtt-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|151411015|gb|EV280826.1|EV280826EST: GGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAG AGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGGCAATCCACTGTTTGA
genomic: GGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtctta ... tatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACACCTAATTCCTGAAAAGACTCCCAGGTCCATTTTTGTTTACTTCCGAGGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtcttatttattacaactcacaaatgtaaaggaggggtggacatgtgaggcttttcatttatttttgcagcatgtctggttaagaccactaacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggtgg