Sequence
atgc intronic sequence ATGC exonic sequence...catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
Basic information
species | Glycine max |
transcript | GLYMA10G27810.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 8
--catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtgc--aatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
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tctgattatgtgcttcaaactttggaagccacaagctcatgatttcatttcctaacacatcgaaaatcgtctcaagttttactttgaatttgtactgt----agGTCCTCAATGCTAAACCAGAGAATGTAGAGAGGGAGGCAGAAATTGTAGCTCAGAGTGGACGCCTTGGTGCAGTGACAATTGCCACCAATATGGCGGGAC
upper sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 9
-----catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
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aatggtgtatgtaaagacaaaccaataaaaaaatcaaat---caattatattccttgtacaagaatactgacagatga-tgttatata-tatgttgtacaaaaagGTCCTCAATGCCAAGCCAGAAAATGTGGAGAGGGAAGCTGAAATTGTAGCACAAAGTGGCCGTTTAGGGGCAGTAACAATTGCCACAAATATGGCAGGGC
upper sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 10
-catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtg--caatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
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atgctatatttatgtttctcttttgctgcc-aacatagcca--aactactatatctaaatattcgttgtatgagatatattaactaatatcatttaattaaagGTTCTCAATGCGAAACCAGAGAATGTAGAGAGAGAAGCAGAAATTGTTGCACAGAGTGGTCGTCTTGGGGCAGTTACAATTGCTACCAATATGGCAGGTC
upper sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------------------------catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttggg---tataaatata-gtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
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gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagactctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatg-attccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTCMapped 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|19934512|gb|BQ079542.1|BQ079542EST: AGAGTGATTCATTATCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAG GTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
genomic: AGAGTGATTCATTATCAGAGCAATTGAAAGAAGCTGGAATTCCGCACGAGgtaaggtccc ... ttgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttgtcttaatttttttgggtataaatatagtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
tcttaat putative branch site (score: 3)
ttgtttct putative PPT
ttaatttttttgggta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttgggtataaatatagtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC
catccat
- - - - -gaaagaac
- - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - -tgcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgcaa