Sequence
atgc intronic sequence ATGC exonic sequence...atcttttgaatgatgatgctctgacaaacttcatgaattattatagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
Basic information
species | Glycine max |
transcript | GLYMA05G27240.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 9
atcttttgaatgatgatgctctgacaaacttcatga-attatta-tagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatc--agGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
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----tctatgcctctatccattggtggcgtacacgatatcatcaatttcttttatttggatttaatactcttgtaaaataaaatgactttggtgctgttctcagGACATTGAATTATCCAAAGAAATAAATGAGTCTTTCAAGCAATCATCTCAAGCAAGGACAAAGCTTCCATCTGGCATTGAAATGAGTGTTCACGTGCTTA
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 9
-----------------------------atcttttgaatgatgatgctctgacaaacttca----tgaattattatagttcttattaacatcacagcttctgacaactacatctcaaatt-tttgtaaatc-------------agGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
|| ||| | | || | | || || || | || || ||| | || |||| |||| || || || ||| | ||| |||||||||||||||| |||||||||||||||||||||| ||| ||||| || || ||| |||| ||| | || || |||||||||||||| ||||| | |
gtagcgttagctgttattactatgaatacatttttagtcttatcttattttgcgaacctgtacagttgtatcgttaggtgcatctgaaatatcaacatttcttttgtatagattcagtatcctttaaacatctgtctggttttgtagGACATTGAATTATCCAAAGAAATAAATGATTCATTCAGACAATCATCTCAAGCTAGGACAAAGCTTCCCTCTGGCATTGAAATGAGTGTCCATGTGCTTA
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 8
--------------------------------------------atcttttgaatg-----atgatgctctgacaaacttca--tgaattatta-tagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaat-cagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
| ||||| | || | || | | | || |||| ||| | || ||||| || ||| | | | ||| | | | | |||||||||||||||| ||||||||||| |||||||||| || ||||| || || ||| |||| ||| | ||||| |||||||||||||||||||| | |
gtagtgttagctgtttctactatgatgatatttctagtcttattttattttgcacacctctatagttctatcgttagatgcatctgaaatatcaatatttctttatatagattcagtgcccttttaacatctcttattacctgctggttgtagGACATTGAATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTA
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
atcttttgaatgatgatgctc--tgacaaacttcatgaattattata-gttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
| | ||||| ||||| | | || ||||| | | || || | ||| | | ||| || | | | | | | ||||| |||||||| ||||| ||||| || || ||||||||||| || || ||||| || ||||||| |||| || ||||| |||||||| || |||||||
---tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
----atcttttgaatgatgatgctctgacaaacttcatgaattatt---atagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
| | | | | | | || || | || | || || |||| | | |||| || | || || |||| | | | | |||||| ||||||||||||||||| ||||| |||||||| || |||||||| ||||| || || ||| |||||||| || |||| ||||| |||||||||||||| ||||
aatgttatatgggtttgtaaatttccatacaagcttataatttgtttgcatagataatgttaa-attattttttatg-caacatcttgtaacattttta-----cagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAAMapped 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|31561323|gb|CD487161.1|CD487161EST: AGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG GACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAG
genomic: AGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAGgtatacatgt ... tgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
tttttgt CT-rich tract
tcaaatttttgtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcttttgaatgatgatgctctgacaaacttcatgaattattatagttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
- - - tgaatga
- - - - - - -tgatgct
- - - - - - - - - - - gacaaac
- - - - - - - - - - - - - - - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactac