Sequence
atgc intronic sequence ATGC exonic sequencegtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
Basic information
species | Glycine max |
transcript | GLYMA17G15740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g43470.1 (Oryza sativa), 3'ss of exon 3
------gtactgatttca-caacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
| ||| || | | || || || | || || | || | ||||| | | || || || ||||| |||||||||||||||||| || |||||||| |||||||| ||||| || || || || ||||| || || ||||| |||
gtgagtcatccaattccatctgccttataatttatcatctgctgtcttcatactctgcttcttctttacatgtttctgaaaattttattt-----tcaactgtc--acagACCATGGCATGGATACTAGATGAATACTCAAAGTTCCATGGCCACTCCCCAGCTGTTGTCACGGGAAAGCCAATT
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT----
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-------------------gtatattctgctttctctagtatttttctactacttcccttcatcatgtaacatcccctgtaattttgac----------acagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
||| ||| | | || | | | | | | | | || | | | || ||| | | ||| |||||||||||| |||||| | ||||| || || || || ||||| |||||||| |||||||| || |||||||| ||
-------------------gtatattctgctttctctagtatttttctactacttcccttcatcatgtaacatcccctgtaattttgac----------acagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
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------------gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtttttcatttgtacctt----ttatgcaattgt--gacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT-------------------------
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------------gtaggcctaacattgcttttgttatttttttttgtatgctcagctatcttgtttttcatttgtacctttt-----atgcaat-tgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 1
--------gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaat---agcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
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gttttccattcctgaatctaatatgtagtgtgtcctttccaggaaaaaaaatattgactctttgacctttctttaacttgaattttactttcct--tactctcgatttggacagACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATT
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36430 (Selaginella moellendorffii), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
|| | |||||| | || | ||| ||| || | | || | |||| || | | | || ||||| | || |||||||||||| |||||||| ||||| || || |||||||||||| | || || ||||| || || || ||||| ||
gtttttttttcacttttttttgttctttcttttatt--tttcatttttttgtttcttttacaaagttggat---ttttatttttttggt----ttcttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
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------------------gtttttttctttttcttttgttctttctttcttttctttttttgcaaagttggattttcattttttttgtttc-----ttcacagACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT
upper sequence: GLYMA17G15740.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 3
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
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--gtttttctctcttttctttggtttttcctctacttgtcctttct------tttctttgggaagttggat------tttcatgtt--tttgtttcttcacagACCATGGCATGGATTCTTGACGAATACTCTAAGTTCCACGGGTATTCGCCAGCAATAGTAACTGGAAAGCCACTTMapped 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|13478706|gb|BG508074.1|BG508074EST: TTGGCGTTCAGAGGGATGTTCCTGCCCCTGATATGGGAACTAAAGCTCAG ACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCA
genomic: TTGGCGTTCAGAGGGATGTTCCTGCCCCTGATATGGGAACTAATGCTCAGgtactgattt ... tgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
aatagtttcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgatttcacaacacagtacatttctgtccatttattttatctaaaaaatagcattcaatagtttcatatatcctttcttattggtccactgtttgacagACCATGGCATGGATTCTTGATGAATATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG