Sequence
atgc intronic sequence ATGC exonic sequencegtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
Basic information
species | Glycine max |
transcript | GLYMA19G36120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g57540.1 (Oryza sativa), 3'ss of exon 2
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattt--tctgtcctcgacgatttcctgacattcacttttcat-aactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
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--------------------------------------------------------------------------------agatgctatttttgtgcctatattgcatatatcgttga-ggccaacaatcatcaactacttgttaaatcttatccactggaactat-tttgtgctttgg-----tagGAGATACTTGAAGGAGTCACGGATATTGATTTGGTCATCAACCTCAAACTCCGAGAAGAGGCTCTGCTTGCAAAATGCCTTGGTAGAAGGATGTGCAGCC
upper sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G150014_T03 (Zea mays), 3'ss of exon 2
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
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-------------------------------------------------------------------atccctggattt--ctatctcaac-----gttataacttgtgtc------aaaccttagacactggggta----gactgcttggtcctaatactggttttatcatgtgccctgtcagGAGATACTTGAAGGAGTCACAGACATTGATTTGGTGATCAATCTCAAACTCCGAGAAGAAGCTCTGCTTGCGAAATGCCTTGGCAGGAGGATGTGCAGCC
upper sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G347841_T01 (Zea mays), 3'ss of exon 2
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaacta-accacacaagtggctatattttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
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------------------------------------------------------------------------------tatccatgccattcaacct-taacatcaacatgtgttgaagaactttagagactgggt----agaattgtagg--gcctaatattgttttatcatgcgccttgtcagGAGATACTTGAAGGAGTCACAAATATTGACTTGGTGATCAATCTCAAGCTTCGAGAAGAAGCTCTGGTTGCAAGATGTCTTGGCAGAAGGATGTGCAGCC
upper sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G081387_T01 (Zea mays), 3'ss of exon 2
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
| | | | | | || | || | || || |||| || | || || | ||| || || | || | |||||| ||| | ||||| || || | |||||||||||| ||||||| ||||||| |||||||| || |||||| ||| ||||| ||||| || || | |
--------------------------------------------------------------------------gcattgaacagtgg-attggtatccatggcattcaatcttaaca-----tcaacatgtg--ttgaagaattgtagg--gcctaatattgttttatcatgtgccttgtcagGAGATACTTGAAGGAGTCACAAATATTGACTTGGTGATCAATCTCAAGCTCCGAGAAGAAGTTGTGGTTGCAAGATGTCTTGGCAGAAGGATGTGCAGCC
upper sequence: GLYMA19G36120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g03360.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctat-attttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
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------------------------------------------------------------------------tgagaata-ttatccccttgctttgttgtcgttttgtctctatggacactttctatc-tatgctcttcataattt---tctttctctcttttggttaa--------ttttcagGAAATATTGGAGGATGTAACTGACATCGATTTGGTAGTTAACCTGAAACTTAACGAAGAAGCATTGCTCGCTAAATGCCTTGGTAGAAGGATCTGTAGTGMapped 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|209697937|gb|BW670139.1|BW670139EST: GCGAATCAGGATTTATTCTTGATGGTTTTCCTCGAACAATAAATCAAGCA GAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
genomic: GCGAATCAGGATTTATTCTTGATGGTTTTCCTCGAACAATAAATCAAGCAgtgagtattg ... gtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
EST:
gi|192315466|gb|FK009674.1|FK009674EST: ATTCTTGATGGTTTTCCTCGAACAATAAATCAAGCA GAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
genomic: ATTCTTGATGGTTTTCCTCGAACAATAAATCAAGCAgtgagtattg ... gtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
EST:
gi|192315467|gb|FK009675.1|FK009675EST: TCTTGATGG-TTTCCTCGAACAATAAATCAAGCA GAAATA-TGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
genomic: TCTTGATGGTTTTCCTCGAACAATAAATCAAGCAgtgagtattg ... gtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
tcataac putative branch site (score: 2)
tacttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtattgatacccacctaatgcccttatattaattagtatatgtgcttgtagttggctgtgatttttcttgggactaactaaccacacaagtggctatattttctgtcctcgacgatttcctgacattcacttttcataactgcgatctacttaaaatgtgcttgaaacctgtgtgctcagGAAATATTGGAAGGGGTAACTGACATTGACTTGGTGGTCAATCTGAAGCTCCAAGAAGAAGCACTGCTTGCAAAATGCCTTGGTAGAAGAATTTGTAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC