Sequence
atgc intronic sequence ATGC exonic sequence...atggtgtttattttgtgttcatggcgtcctgtagacatgtggttgtaatgttttactaattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
Basic information
species | Glycine max |
transcript | GLYMA16G29450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 1
---------atggtgtttattttgtgttcatggcgtcctgtagacatgtggttgtaatgttttactaattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
||| || | |||| || || ||| || | | | | || || | ||| | ||| || | ||| | ||| |||||||||| |||||||||||||| || |||||| | | | || | | || || ||| | || |||||
ggtgctaaaatgac-ttagctgcatgtttattttgttttgtt----tgcaaagacattatcatgctgttt--catattaaagcaacaaattgcactttgtcttg--cagAGGCTGTAGCTGATGCTAACAAGGCCATTGAACTTGACCCATCAATGCACAAGGCTTATCTTCGTAAAGG
upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 1
atggtgtttattttgtg-ttcatggcgtcct-gtagacatgtggttgtaatgttttact-aattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
|| | | | |||| | | | | | | | | | || || ||| | | || || |||| || || ||||||||||| || ||||||||||||||||||| | || || | | | ||||| || | ||||||||
atagacacagtctaacaactcatactaccatcattggcttccatatttgtttttaaacagaataaatgtatcacactaaaggaattaactaaactt---gcagAGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG
upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 1
atggtgtttattttgt-gttcatggcgtcct-gtagacatgtggttgtaatgttttac-taattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
| |||| | || |||||| | | | | | || | | | || || ||| | | ||| || ||| || || |||||||||| || |||||||||||||||||||| | || || | | ||||| || | ||||||||
tttcagtttgtagcgttattcatgctaccatcattggcttgcatatttggttttaaacacaataaatgtattgcactaatggaatcaactaaacttc---cagAGGCTGTGGCGGATGCTAACAAAGCAATTGAGCTTGATCCTATGATGCATAAAGCTTACTACCGGAAAGG
upper sequence: GLYMA16G29450.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 1
atggtgtttattttgtgttcatggcgtcctgtagacatgtggttgtaatgttt------tactaattactaaattttgggaactaaattttcttgctttt-gtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
||| | ||| || |||| | | | | | || ||| | || ||| | | ||| |||| |||| |||| | |||||||||||||||||||| |||| ||||||||| ||| | | || | | ||||||| |||||||||||
------tttgtcttg-atttatggtaccattcacatttttgcacaacatgcaaatcaagttctccttatgagaggctggtggctaactttttcaattttttgagcagAGGCTGTTGCTGATGCAAACAGAGCAATTGAGTTGGACCCATCAATGTCTAAAGCATTCTTGCGGAAAGGMapped 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|193455369|gb|FK419290.1|FK419290EST: ACTCTACGCCGACCGAGCCCAAGCCAACATCAAACTCTACAACTTCACTG AGGCTGCTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAA
genomic: ACTCTACGCCGACCGAGCCCAAGCCAACATCAAACTCAACAACTTCACTGgtacaccatc ... ttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAA
EST:
gi|7145795|gb|AW507717.1|AW507717EST: ACTCTACGCCGACCGAGCCCAAGCCAACATCAAACTCAACAACTTCACTG AGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAA
genomic: ACTCTACGCCGACCGAGCCCAAGCCAACATCAAACTCAACAACTTCACTGgtacaccatc ... ttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgttttactaattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
ttttcttgcttttgt CT-rich tract
ttttactaattactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtgtttattttgtgttcatggcgtcctgtagacatgtggttgtaatgttttactaattactaaattttgggaactaaattttcttgcttttgtgcagAGGCTGTTGCTGATGCTAACAAAGCAATTGAATTGAATTCTTCTCTACCAAAAGCATATTTGCGGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
-tggtgtt
- - - - - - -tgtgttc
- - - - - - - - - - - - - tcctgta
- - - - - - - - - - - - - - - - - - - gtggttg