Sequence
atgc intronic sequence ATGC exonic sequence...attggacgggaaatgcaaggttttgatatgatataaaaattaataatattgatcatgtaaactaaatagttttttgttatttgaattatttgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA18G47980.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 6
attggacgggaaatgcaaggttttgatatgatataaaaattaataatattgatcatgtaaactaaatagttttttgttatttga---attatttgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
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-atatgtacacggctcatgttaactgtatatgcttaaattttgtagtgatattttggtgttccaa-tgttgtaatatagattaacatataatttttgagcagGCACCATCAGCATGGGAGATGGCAAGCAAGGATAGGGAGGGTTGCAGGAAACAAGGACCTCTACTTAGGCACCTTCA-
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------attggacgggaaatgc---aaggttttgatatgatataaaaattaataatattgatcatgtaaactaaatagttttttgttatttgaattatttgattg--cagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
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gtaattaaacttcactagtaggcaatgtatgatttgtgtgcatacaaaaaaattgtccttttatttcacattatcattagatgcctgttgtgggaaaaacataactttacaagagatttatggaacttgtttttgtttcctttttt-tatattgacatcaatgttgtt-aatcgatcagACATCATCAGCATGGGAGATGGCAAGCAAGGATAGGGAGAGTTGCAGGAAACAAGGATCTTTACTTGGGCACATTCA-
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G17430.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------attggacgggaaatgcaaggttttgatatg-atataaaaatta----ataatattgatcatgtaaactaaatagttttttgttatttgaattatttgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
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gtacgtataatccatctagatatggaacgaatacagtgtttcattattttttttgatgtatacataataattgtcatacaatactattaatctaatctaattaatatttcct--ttaaaatggttcca--aaagGCATCACCAACATGGAAGGTGGCAAGCTAGGATCGGAAGAGTCGCCGGTAACAAAGACCTCTACTTGGGAACTTTCG-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|14258884|gb|BG881792.1|BG881792EST: AGAGTAGTGGGTTTTCTCGCGGGGCATCCATTTATCGAGGTGTGACGAGA CACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAAC
genomic: AGAGTAGTGGGTTTTCTCGCGGGGCATCCATTTATCGAGGTGTGACGAGGtacagttcac ... tgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgatcatgtaaactaaatagttttttgttatttgaattatttgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
taaactaaatagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attggacgggaaatgcaaggttttgatatgatataaaaattaataatattgatcatgtaaactaaatagttttttgttatttgaattatttgattgcagaCACCATCAACATGGAAGATGGCAAGCGAGGATTGGAAGAGTTGCTGGCAACAAGGATCTCTACTTGGGAACTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- -ggacggg
- - - - - - -tgcaagg
- - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgtaa