Sequence
atgc intronic sequence ATGC exonic sequence...ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
Basic information
species | Glycine max |
transcript | GLYMA14G40270.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 19
-------ttaagac-ccggaccattatacaaaaggattgtggcaaatgttattaatctctttctatgta------------ttcatgccaagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
||| | | | | |||| || || | | | ||||| ||| | | | |||| | |||||| |||| || || ||||| |||||||| ||| | ||||||||||| || |||||||| ||||||||||| || || || || ||| ||| || ||||| || || | ||||| |
gtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctcttt----ctatgtattcatgccaagcctaa--catgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
| | | | | | ||| || | ||| || | | | | | | ||| | |||| | ||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||||||||| || || ||||| || |||| |||||| |||||||| || | ||||| |
------cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM5G844195_T04 (Zea mays), 3'ss of exon 2
----------------------------------------------------------ttaagacccggaccattatacaaaaggattgtggc--------aaatgttatt-----aatct-ctttctatgtattcatgccaagcct---------aacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
| | || | | | || |||| || | ||||||| |||| |||||| | || | | ||||| | | |||| |||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||| ||||| || || ||||| |||||| |||||| ||||||||||| | ||||| |
gtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 19
ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
| | ||| | | || | || | || ||| | | |||| | | || | || || | || | | | | | ||||| ||||||| |||| | ||||| ||||| || |||||||| ||||| ||||||||||| ||||||||||| ||||||| ||||||||||||||||||||
-----gtacaaat-attttgccaatgatttctc----attttacaagctttcttctcaatttctatccaaacgcttatat-----tttctttgtgaccagTACTCAGCAAGGCTTCTTAAGAAGCCTGACCAATGCCGAGCGGTTTACGCATGCTCTCACCTCTTTTGGGTCGATGATCCAGATGGTATTAAAGATGGAG
upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 19
ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctctttctatgtattcatgcc-aagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
|| | |||| || | ||| || | || || | || | | | | || || ||| | ||| || || |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||||
gtagtaatgtttacattctatctgattattttgac-----ttgttgaactttctatgccaaaagttgtttaaaccttttccttttgtctttccttggccagTATTCAGCAAAGCTTTTAAAGAAACCTGATCAATGCAGAGCAGTTTATGCATGTTCCCATCTTTTTTGGGTTGACGATCAAGATGGCATTAAGGATGGAGMapped 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|51335912|gb|CO979778.1|CO979778EST: ACATCTTTGGCGTCGAGAACAGGGATACATTAACACACAAGGCCACAGGG TATTCAGCAAAGC-TTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCA
genomic: ACATCTTTGGCGTCGAGAACAGGGATACATTAACACACAAGGCCACAGGGgtatagtctg ... cttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCA
EST:
gi|14011807|gb|BG726729.1|BG726729EST: ACATCTTTGGCGTCGAGAACAGGGATACATTAACACACAAGGCCACAGGG TATTCAGCAAAGCTTTTGAAGAAA
genomic: ACATCTTTGGCGTCGAGAACAGGGATACATTAACACACAAGGCCACAGGGgtatagtctg ... cttttcacagTATTCAGCAAAGCTTTTGAAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctctttctatgtattcatgccaagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
gcctaac putative branch site (score: 2)
tgctctatcttttc putative PPT
tatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct