Sequence
atgc intronic sequence ATGC exonic sequencegtaaacttctttacctctgaaaatctgtagtaaaaataattatcaattggtatcatttatgttgctggatggatgtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA16G28980.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------gtaaacttctttacctctgaaaat-ctgtagtaaaaataattatcaattg-----gtatcatttatgttgctgga-tggat-gtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
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gtatgatgcaatcgatcatattgctcgtactccattgtgctaacatgtccattacaacctgaggcttgaaaaagccattactttggttgtttccgtactttctagatctataatttgtccaggaaatagtcttcatgctggaatgcattaacatacaaacagcagtcttagaattttctgtgtcttcatgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGAAAAGCTGTTATTGTTGCCACTAATATGCTAGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG
upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 7
gtaaacttctttacctctgaaaatctgtagtaaaaataatta-tcaattggtatcatttatgttgc---tggatggatgtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
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---------------------agtgcttactataagctgtcagtaaagaaatattttttcctttgccgatgaaggtgtttcagatttacatcttccttgaat-attatgttctttcctgcagGAAGAAATTATTAGAATGTGCAGGAGCATGGGGAAGGCTGTTATTGTTGCTACAAATATGCTCGAAAGTATGATTGTTCATCCAACTCCAACCCGAGCAG
upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaacttctttacctctgaaaatctgtagtaaaaataattatcaattggtatcatttatgttgctggatggatgtcatgttgagctc--atcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
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-------------------------gttagtacttgcctctcatttttaagataacccagagaaggagatttagaacttgttgaagttgaaactcttgattttaat--ttgttat-acagGAGGAGATCATTAACCTGTGCCGTAGTATGGGAAAAGCTGTTATTGTTGCGACTAACATGCTTGAGAGTATGATAGTTCATCCAACTCCAACCCGGGCAG
upper sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 7
gtaaacttctttacctctga--aaatctgtagtaaaaataatta-----tcaattggtatcatttatgttgctggatggatgtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
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gtaa-tttctttgtttctgattgaagagatgatagagataatagggtcttccagaagtgcctttcatgttttataacaagcatctacttgagtatttaccaacatttcaa--------actgcagGAAGAGATAATCAGGATATGTCGTAGCATGGGAAAAGCTGTTATTGTAGCAACCAATATGCTGGAAAGCATGATTGTTCACCCAACACCAACCCGAGCAGMapped 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|23734545|gb|BU765511.1|BU765511EST: GAGGAGATCTTGGCGCTGAGCTCCCTATTGAAGAGGTTCCACTTTTGCAG GAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCA
genomic: GAGGAGATCTTGGCGCTGAGCTCCCTATTGAAGAGGTTCCACTTTTGCAGgtaaacttct ... gttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctggatggatgtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
tcttaac putative branch site (score: 2)
ttattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacttctttacctctgaaaatctgtagtaaaaataattatcaattggtatcatttatgttgctggatggatgtcatgttgagctcatcttaacatcgtaatggctgttattgtagGAAGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG