Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgttcttttactcttcctcaacaggaatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
Basic information
species | Glycine max |
transcript | GLYMA18G16160.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5
gtgtgttcttttactcttcctcaacaggaatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT---------------------------------------------
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--------------------------------------------tttcattgatttaactgttcagtacttctatttcctgctttgtattat-ttccagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA
upper sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5
---gtgtgttcttttactcttcctcaacaggaatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
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acaatgcata-tttcatggactcaagacattgacatattacaggcaatttcattgatttaactgttcagtacttctatttcctgctttgtattat-ttccagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA-
upper sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
gtgtgttcttttactcttcctcaacaggaat-atagtgttgacttgtacattgctctggattct-tgctattttttcattaaattggctttcttg----ttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
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-----tgccatcgctgtttatgaattattatgatgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG-
upper sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgttcttttactcttcctcaacagg-aatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttctt-----gttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
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-----attttggattaaagaacaatttataatggctttttatagtgtagcttgctttgtgagaatttggattgctaattatgttgccttcctcttatgattgcagTCGCTGCTTTGTGACCCAAACCCAAACTCTCCTGCAAATTCAGAAGCAGCACGGATGTTTAGTGAGAACAAGCGTGAATACAACAGAAGAGTGCGTGAGA-
upper sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 6
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtgtgttcttttactcttcctcaacaggaatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
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gcgagagtggatggcttcttcttcagcgtgtgca-gccgaacacagcgatgatgacgacgatgcgtgaaagctgtttctctaacacgtggctttggtgcagTCTTTGCTATGCGACCCAAACCCGAATTCACCAGCAAACTCGGAGGCTGCTCGCATGTACAGCGAGAACCGGCGTGAATATAACCGGAGGGTACGCGAGA-Mapped 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|19346345|gb|BM891225.1|BM891225EST: CAGGGAAACCTAAACTTTGATGTGAATTTCACAAGTTACTACTAGTTCTT CATTGCTGTGTGATCCAAACCCAAATTCA
genomic: CAGGGAAACCTAAACTTTGATGTGAATTTCACAAGTTACTACTAGTTCTGtatgtcacct ... ttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
ctttcttgtt CT-rich tract
ttgctattttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttcttttactcttcctcaacaggaatatagtgttgacttgtacattgctctggattcttgctattttttcattaaattggctttcttgttgcagtCATTGCTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGTGAAAACAAGCGTGAATACAACAGAAGAGTACGTGAGAT
-tgtgttc
- - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - -tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - ctctgga