Sequence
atgc intronic sequence ATGC exonic sequence...tacgcgaggaatgtcataaatgccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
Basic information
species | Glycine max |
transcript | GLYMA17G16420.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 4
tacgcgaggaatgtcataaatgccatgaacatcattggttcatta--gtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
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-atctgtagttgcctatgtggttttttacctgttgtaattgattattgtagctgcctaaggaatacatcgcctgttgtaaccgatttctat-tccctatcagGAAGGTGATCCCCGCCTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGAAAAAGCTATAGTACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
----tacgcgaggaatgtcataaatgccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
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atatgaagttgccaatgtgatttttcacctgt-tataattgattatct--tagctgcctaaagaatacctcacctgttgtaatcaatttctat-tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g01140.t01 (Vitis vinifera), 3'ss of exon 4
----tacgcgaggaat--gtcataaatgccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
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aatgtagatatgcatttagatcttattctcatgcacatcttgtggccaccaaattctctctatcct------catactttataactaaattttgcacttgtgtcagGATGGTGACCCTCGTTTATCAAGTTTTGGCCTTATGAAAAATAGTCGAGATGGTAAAAGCTACAGTACAAACTTGGCTTATACTCCACCAGAGTTTTTGC
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
-tacgcgaggaatgtcataaat--gccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
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ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggtt---agtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
upper sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 4
tacgcgaggaatgtcataaatgccatgaacatcattggttcattagta-catgtctaaattatggattga--aatttgttactaatttatt-catttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
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-tcgtgtgggtttcctttg--gaaatagttctacttagtacgtggatttcaactgcagttaatagaatgctcagtatattaacgattctctacgattttgt-agGACGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGAAAAAGCTACAGCACCAATTTGGCTTACACTCCTCCTGAGTACTTGAMapped 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|8401818|gb|BE057452.1|BE057452EST: ACCGTAAAATATATCATGATCTGAATGCATATAGGATTCTNTNTGATGAG GATGGTGATCCACGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGAT
genomic: ACCATAAAATATATCATGATCTGAATGCATATAGGATTCTTTTTGATGAGgtaagattat ... tttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
tactaat putative branch site (score: 1)
ttcatttct putative PPT
taaattatggattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacgcgaggaatgtcataaatgccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC
- - - -ggaatgt
- - - - - - - - taaatgc
- - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - -acatgtc