Sequence
atgc intronic sequence ATGC exonic sequence...tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattatctctctgtctctatcaatatcatcaatttcttgctgcatcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
Basic information
species | Glycine max |
transcript | GLYMA13G31380.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 4
tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattat-ctctctgtctctatcaatatcatcaatttcttgctgcatcatgtatgc-agGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
| | || | | | ||||| | || | |||| ||| | ||| || | | || || || || ||| | || || | | |||||||||||||| || ||||||||||||||||||||||| || ||||| || || || || || || || || ||||||||||| |||
gtaagtactagtttcagcgcggcactgtctgttc----cagcagggttatgttcttagcatctgattattttgcctcgttgtttatgggggat-tatactagAGAAGGTGACCTTCCTCTTATTGTTGCCATTGATTTGCAACCAATGGCTCCGATAGAAGGCGTTATACAAGTTCAAGGGGACATCACTAATGCTCGAACA
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G083745_T03 (Zea mays), 3'ss of exon 4
------tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtat-tatctctctgtctctatcaatatcatcaatttctt--gctgcatcatgt-atgc----agGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
| | | | | | | ||| | | || |||| ||||| | ||| | | | | || | | | | |||| ||| ||||| | |||||||||| || || || ||||| |||||||| ||||| ||||| |||||||| || || |||||||| || || || ||||||||||||
gtaagagtcagtgcctgtgtgtcgcagtctgttcttgcatagttctgttgtggatatctgatggcctcgttttgcacttttgctctccttggttctgttatgttgtgctactagGGAAGGTGATCTTCCTCTCATCGTCGCAATTGACTTGCAACCGATGGCCCCAATAGAAGGTGTTATACAAGTGCAGGGCGACATCACCAATGCTCGGACA
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 5
------tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgt-attatctctctgtctctatcaatatcatcaatttcttgctgc---atcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
|| ||| || | || | || | || || | || | || | | | | |||| || ||| | || ||||||| |||| ||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||||| || || || |||||||||||||||||
gtaagtttctcttccaccatcgtttttctttagttgttttaatctgctagttagtaatccactatttgacaaggttgaactgatttgttactgttgaaacac-tatgcagAGATGGGGATCTTCCTCTTATAGTAGCCATCGATTTGCAGCCTATGGCTCCAATTGAAGGTGTCATCCAGGTTCAAGGGGACATAACTAATGCTCGGACT
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 4
tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattatctctctgtctctatcaata--tcatcaatttcttgctgcatcatg-tatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
| | | | ||| | |||| |||| || | | | | | ||| | | || || || || |||| | | |||||||| |||||||||||||||| || ||||||||||| || ||||||||||||||||| || || || || |||||||||||||| |||||||| |||
---cgggcctcaagggcttctaattgttactattatgtcaccctctttttgtgtaggaccttattgtcaagctaataactttttacttaatcaaaattttcagGGATGGTGATCTTCCTCTTATTGTGGCGATTGATTTGCAGCCCATGGCTCCAATTGAAGGGGTGATTCAAGTCCAGGGTGATATAACAAATGCTCGTACA
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ27494 (Selaginella moellendorffii), 3'ss of exon 4
tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattatctctctgtctctatcaatatcatcaatttcttgctgcatcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
| | | || ||| || |||||| | | | | |||| | ||| | | | ||| | || | | ||||||||||| ||||||||| |||| |||||||| || ||||| |||||| | || | || || || || |||| ||| || ||
--------------------gtaagagctttgc-------cttcctttttctctcctttctttgtgaggaaaaagatttatcactgtgttct---tctagGCAGGATGACCGACCTCTTATTGTGGCTATTGATCTGCAGCCAATGGCCCCTATTGATGGTGTCGTTCAAATTCAAGGAGACATCACTAGTGCACGAACT
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ07303 (Selaginella moellendorffii), 3'ss of exon 4
tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattatctctc-tgtctctatcaatatcatcaatttcttgctgcatcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
| | || | | | || ||| || |||||| | ||| | | | | | |||| | ||| | | | ||| | || ||| ||||||||||| |||||||||||||| |||||||| || ||||| |||||| | || | || ||
-------------gtgataagtaagagctttgc-------cttcctttttctctcctttctttgtgagga--aaagATTTATCACTGTGTTCT---TCTAGGCAGGATGATCGACCTCTTATTGTGGCTATTGATTTGCAGCCAATGGCCCCTATTGATGGTGTCGTTCAAATTCAAGG----------------------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|151401979|gb|EV271792.1|EV271792EST: GTTTTGAGTCGTAAATTGTATCTACCAGCCAAGCTTGCACCTGATGCAAA GGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCC
genomic: GTTTTGAGTCGTAAATTGTATCTACCAGCCAAGCTTGCACCTGATGCAAAgtaagttggc ... atgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatctctctgtctctatcaatatcatcaatttcttgctgcatcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
aatatcatcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctttcttttattaaaaaaaatgtgtcttattgaatcacttgtattatctctctgtctctatcaatatcatcaatttcttgctgcatcatgtatgcagGGATGAAAATCTTCCTCTTATTGTAGCTATTGATTTGCAACCAATGGCTCCAATTGAAGGTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - -aaaaaaa
- - - - - - - - - - - - gtgtctt
- - - - - - - - - - - - - - - - - - - cacttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc