Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
Basic information
species | Glycine max |
transcript | GLYMA20G37360.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtac-tgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttga--ttaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
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---------------------------------------gtatgtgcttttttttggctgatttcagttgctcat-ttgttcatttgcatgatccgccacaatcagaaacatactcctagaac-aatgttaagctcacagctcact----cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttga--ttaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
||||| | | || || | | | | || || || | | | ||| | | || || |||||| | | | | | || ||| | | |||| ||| | |||| || ||||||||||| |||||||||||||||||||| ||||| |||||| | ||||| ||||| | ||||||||| | ||| |
------------------------------------------gtgcttttttttggctgatttcagttgctcat-ttgttcatttgcatgatccgccacaatcagaaacatactcctagaac-aatgttaagctcacagctcact----cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
| ||| ||| ||| ||||| | || | |||| || || | |||||| || | |||| || | | ||||| |||| | ||| | || ||||||||||| || ||||||||||||||||| ||||| || ||| | ||||| | | || || | | |
---------------------------------------------------------------ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaa-tgtaaattttgcaatgtctctaatttgtcccatttattt-atatcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGTCTCTTTGGTTTCTACAAATCACA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgtt-ttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
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---------------------------------------------------------------gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagt-atcgctgatttgtgctaatcctttt--ttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
||||| ||| || ||| | | || | ||| | | | || || || || ||| ||| | | | | | | | | || || | | || | | || | | || | ||||| ||| | || || |||||||||||||||||||||||||| |||||||| |||||||| ||| | || || ||| |||||||| ||||| | ||| |
gtatgctaa------ttccttatttatttcagttacttagcagt-------tcattggcatgaacttc-tttgcatataccgtgttgcgtagcatctggacctg-gacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgctt--ctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
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-------------------gtacattcctatatttatttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatctggaagggtgcc---aaatcttgtctcttggctaacacaattcttcatcttttctctcttatcta-cagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 6
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgtt-ttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgt-gtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA---
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------------------------------------------------------------------tcttatcggccatggtccaaaaggaagcccatactatcataaaacaaactttgcagt-atcactgacttgtgcttatccttttttttttgtcttaccacagAAACGAAGGTTCGTCACTCATGCA---GCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCTTTGGACACTTCAAATC
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA
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-----------------------------------------------------------------tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGG-ACAGC--TTGGCTTTCCTTTGGGATCTTCTA
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--------------------------------------------------------------tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatcctttttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------
upper sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 9
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
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--------------------------------------------------------ttgagagcttttgtttcttttttatgtttgcaatcacccgagtccttgcaacc-agagttcga--------ttgtttgaatttgttttccgtgtttctttctgaaacagCGAAGACGCCTAATCTCCCATGCAAATGCAAAGAGTAAGAGTGAAAAGTTTCCTCCACCTCACCAGGACGGAGCAGTTGGCTTCCCCTTGGGTGCTTCACMapped 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|6667897|gb|AW279348.1|AW279348EST: AAGCTGCTCCTGCTCGTGAAGGCAATGCTGAGCTTCAATCCAACATTGAT AGAAGGCGTTGAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTA
genomic: AAGCTGCTCCTGCTCGTGAAGGCAATGCTGAGCTTCAATCCAACATTGATgtatgttaaa ... tgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
ataaaattaatgttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA