Sequence
atgc intronic sequence ATGC exonic sequence...ttcaatattgtgtcgtatgaaggtggtaagtaaataaagaaaattgatatcggtgatgattgtttgtttgtggtgtgcgttaacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
Basic information
species | Glycine max |
transcript | GLYMA19G02150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g36848.1 (Oryza sativa), 3'ss of exon 1
ttcaatattgtgtcgtatgaaggtggtaagtaaataaagaaaattg-atatcggtgatgattgtttgtttgtggtgtgcgttaac-attacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
| ||| || | | || || | || |||| || ||| | | | | | | || || | || || || | ||||||||||||||||| || ||||| ||||| ||||| |||||||||||||| ||||||||| | ||| ||||| || || | || || || | |
gtaaattttctagtctctgccactgattag-aaatggagggaataataagtaaacaacaagtagt-gtgagtaataagcaaaggtgatgacgtggcatgcagGACGTGATGTTCGGGGGGACGGAGACGGTGGCGTCGGCGATCGAGTGGGCGATGGCGGAGATGATGCACAGCCCCGACGACCTCCGCCGCGTGCAGGAGG
upper sequence: GLYMA19G02150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g02180.1 (Oryza sativa), 3'ss of exon 1
ttcaatattgtgtcgtatgaaggtggtaagtaaataaagaaaattgatatcggtgatgattgtttgtttgtggtgtgcgttaacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
|| | | | | || || || | ||| | | | ||| | || | |||||| | | ||||| || ||||| ||||| ||||| |||||||||||||| ||||||||| | || ||||| | |||| |||| | || |
----------------------gtacgtgccattctgacaccactgccat-ggcatgcacgtcgcgttgcttgatggagttggcg--acgacaagtgcagGACTTCGTCTTCGGCGGGACGGAGACGGTGGCGTCGGCGATCGAGTGGGCGATGGCGGAGTTGCTGCACAGCCCCGGCGATCTCCGGCGGCTGCAGGCGG
upper sequence: GLYMA19G02150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G100158_T01 (Zea mays), 3'ss of exon 1
-ttcaatat-tgtgtcgt-atgaaggtggtaagtaaataaagaaaattgat-atcggtgatgattgtttgtttgtggtg-tgcgttaacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
||||| | || || | | || ||| | || || | | || | ||| | | || || | || || ||||||||||||||||| || ||||| ||||| ||||| |||||||||||||||||||||||| | ||| ||||| || || | ||||| || || |
gggtaatatgtacctcaccatcgcgtcgttatgtattttgttgttttttatgagcagtcaaagctgtaaactaataatgatgtatggacgccgca-----tgcagGACGTGATGTTCGGCGGGACGGAGACGGTGGCGTCGGCGATCGAGTGGGCCATGGCGGAGATGATGCACAGCCCCGACGACCTGCGCCGGGTGCAGCAGG
upper sequence: GLYMA19G02150.1 (Glycine max), 3'ss of exon 2
lower sequence: AC210173.4_FGT005 (Zea mays), 3'ss of exon 1
ttcaatattgtgtcgtatgaaggtggtaagtaaa--taaagaaaattgatatcggtgatgat-tgtttgtttgtggtgtgcgttaacat-tacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
| | || | ||| |||| | ||| |||| ||| | ||||| || | | | | || |||| | | | |||||||||||||| || || ||||| ||||| ||||| |||||||||||||| ||||||||| | ||| ||||| || || | ||| | || || |
---gccagattctcaga-aaagctggtcaaaaaagctaaaccaaacagcccctataaatgatgcgtctctatcttttggtcgttgatggacgacgcgtgcgcagGACGTGATGTTTGGCGGGACGGAGACGGTGGCGTCGGCGATCGAGTGGGCGATGGCGGAGATGATGCACAGCCCCGACGACCTGCGCCGGCTGCAGCAGG
upper sequence: GLYMA19G02150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g02900.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------------------ttcaatattgtgtcgtatgaaggtggtaagtaaa---taaagaaaattgatatcggtgatgattgtttgtttgtggtgtgcgt-taacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
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gtaaggatgaaactcacatacaacaaattttgccatctttcacgcttaagaacattttccagaattcaatttctactattgcgagtttcttacttgcaacctgataaaaagagccacctgttctattctaggttttgacaagtcgatgtgatattatatatttc--agGACGTTATGTTCGGTGGTACAGAGACTGTGGCGTCTGCAATAGAGTGGGCCATGGCAGAGATGATGAAAAGCCCAGAAGATCTCAAGAAAGTTCAACAGGMapped 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|10238731|gb|BE807619.1|BE807619EST: TGCAGAACTCTATCAGACTCACTAAGGATAACATCAAGGCTATCATTATG GACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCC
genomic: TGCAGAACTCTATCAGACTCACTAAGGATAACATCAAGGCTATCATTATGgtatggattc ... atttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatcggtgatgattgtttgtttgtggtgtgcgttaacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
cgttaac putative branch site (score: 3)
ttaacattacaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaatattgtgtcgtatgaaggtggtaagtaaataaagaaaattgatatcggtgatgattgtttgtttgtggtgtgcgttaacattacaatttacacagGACGTGATGTTCGGAGGCACGGAAACGGTAGCGTCAGCGATCGAGTGGGCCATGGCGGAGCTCATGAGAAGCCCAGAAGATCAAAAGCGGGTCCAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA