Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
Basic information
species | Glycine max |
transcript | GLYMA16G17580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
---------------------gtgagtatttgttgcagaagcctgaagttactatacccctct----tttttactgtcaaatatct-ttaaggtttttcttccttccgtgaaca-----cagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
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gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
gtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
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----gtaactttcatattgacttactatttttaggtcacctttttct--tatcaagtatgtt----gtcttt---------------gcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 4
gtgagtatttgttg----cagaagcctgaagtta-ctatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
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gtgagaatggtctataaccagacgattataacaaattagaatactgtctaagctgtttggatgtcttcttaccttgtttttgcattgcgctc-cagATATACAATTATCAACGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGCGTGCAACCAATAAGGAAAGCGGTGAAGTG
upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
------------gtgagtatttgttgcagaagcctgaag-ttactatacccctcttttttactg-tcaaatatctttaaggtttttcttccttccgtgaac----acagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
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gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgt-caaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
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gtgagtgggcttgtatggaacttg--cttgtta-atatttgtattttaatgtgttgatatgtctgagagttttggcctct--------acagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
tttttcttccttccgt CT-rich tract
tcaaatatctttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG