Sequence
atgc intronic sequence ATGC exonic sequencegtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
Basic information
species | Glycine max |
transcript | GLYMA13G28720.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
---gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
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gtaacagatttgatatccatattctca--attgatagatc---atgttggttttccttgta-tgatttgtgtaacatgttacacttg--aagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttc-----tatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
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gtgagtaatataac--tcccatgctcaatggctcattatgctaataatttgggaca-acctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaattacagaaccttcttttgattgttggaagtccttaatgtta-atctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
|| || | | || ||| ||| | |||| | || | || || | || | ||| | | | | | |||| || || |||||||| |||||||| | |||||||||||||||||||| ||||||||||| ||||| || || ||||| || || ||||| || ||||
-----gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtag--gttaattgc-tttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
||||| || |||| || | || || | | | | || || |||| | | ||| | || | ||| | | |||||||||| || || |||||||| || |||||||||||||||||||||| ||||| || ||||||||||| || ||||| ||||||||||| ||| |||
gtaaacc-caagacctcctaat--tttttagctctaccttat-ttcatctcatttactgaaatggtttctgtatt-tctgt-tttttagGTCCTCCGGCCTTTCCTCCTTCGGAGACTGAAGTCAGATGTTGAGAAAGGCTTGCCTCCAAAAAAGGAAACAATACTTAAAGTAGGCATGTCTCAATTGC
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 7
gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacata-attgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
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----------------------------------------gtatgaatgagcgctatgcgctatcgtcgatgctgataatg-atttacagGTGTTGCGGCCTTTCCTTTTGCGAAGGTTGAAGTCAGATGTTGAAAAGGGGCTGCCTCCCAAGAAGGAAACAATCCTCAAGGTTGGCATGTCAAAAATGC
upper sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 7
gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacata-attgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
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----------------------------------------gtatgaatgagcgctatgcgctatcgtcgatgctgataatgattttacagGTGTTGCGGCCTTTCCTTTTGCGAAGGTTGAAGTCAGATGTTGAAAAGGGGCTGCCTCCCAAGAAGGAAACAATTCTCAAGGTTGGCATGTCAAAAATGCMapped 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|254345542|gb|GR851704.1|GR851704EST: AAATCTCTGGTGAAAATGACCAACAGGAGGTTGTTCAACAATTACACAAG GTCCTCCGCCCATTTCTCCTTTCGAAGGTTGAAGTCAGATGTTGAGAAAGG
genomic: AAATCTCTGGTGAAAATGACCAACAGGAGGTTGTTCAACAATTACACAAGgtaaattaca ... gtatatcaagGTCCTCCGCCCATTTCTCC-TTCGAAGGTTGAAGTCAGATGTTGAGAAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
tgttaat putative branch site (score: 3)
attttcattttctatg 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
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gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA