Sequence
atgc intronic sequence ATGC exonic sequence...cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaactgtttttgtgcttgctattgttcattaactaaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
Basic information
species | Glycine max |
transcript | GLYMA05G06140.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 8
--cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaa-ctgtttttgtgcttgctattgttcattaactaaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
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ttgctgaaatatttcagaaattatggagtcacattcatttggtttgttaagataagctagttttat-tttgtgcatgtttatgg--tgatgtaaaaactgaagCTGTCCTTTCAAGAATGGACTCAGCAAGTGCAAGAGATGCTGAATACCAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTCAAGACTGCAATTG
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G054634_T01 (Zea mays), 3'ss of exon 8
-------cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaactgtttttgtgcttgctattgttcattaactaaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
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atttgtgtctgcacttgctcaa-gtatttttaaattatcaagtcctacttgtttttttaag-atgagtctatttcgtctggtgcatgttttaaaaac-----tgaagCTATCCTTTCAAGAATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTG
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 8
cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaactgttt-ttgtgcttgctattgttcattaactaaaaatgta---attgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
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--ttgtgtctacacttgctcaagtattttgaaattatgaagtcctact--tgtctgtttattaagataagtttattttgtctgatgcatgtttaaaaactgaagTTATCCTTTCAAGAATGGACCCAGCAAGTGCAAGAGATGCTGAACACAAAGAAGTTTGGTGACATTGCATTTAGAGACAAGGATTTTAAGACTGCAATTG
upper sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 3'ss of exon 8
cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaactgtttttgtgcttgctattgttcattaacta---aaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
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---ttttcatttccctttttatgtttgtctttgatttgtgcttgtgctcttagcagtcctacatcatgatattctgcactgacattgcaatctctatatgtagCTTTCATTTCAAGAATGGACACAACAAGTGCAAGAGATGTTGAACACAAAGAAATTCGGGGATATTGCATTTAGGGACAAGGATTTCAAGAGTGCAATTGMapped 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|14011822|gb|BG726744.1|BG726744EST: GCAGAAAATGAG CTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAA
genomic: GCAGAAAATGAGgtatgtcaaa ... gtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgccaactgtttttgtgcttgctattgttcattaactaaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
aactaaa putative branch site (score: 2)
tattgttcattaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacaaaattgttaattgtttatcctacttgttaatctcaggttgttttgccaactgtttttgtgcttgctattgttcattaactaaaaatgtaattgcagCTTTCATTCCAAGAATGGACACAACAAGTGCAAGATATCTTGAACACAAAAAAGTTTGGGGATATTGCATTCAGAGACAAGGATTTCAAAAATGCAATTG
- - - - - - - - - - - -ctacttg
- - - - - - - - - - - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgct