Sequence
atgc intronic sequence ATGC exonic sequence...tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
Basic information
species | Glycine max |
transcript | GLYMA07G05170.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
------------------------------tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacc-catattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
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gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaattt--aatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
| | | | | | || ||| | ||| | | | || | ||| |||| || || | |||||||||||||||| ||| ||||||||| ||||||||||| ||||
--ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116919_T02 (Zea mays), 3'ss of exon 5
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaattt--aatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG------------------------------------------------------------
| | | | | | || ||| | ||| | | | || | ||| |||| || || | |||||||||||||||| ||| ||||||||| ||||||||||| ||||
--ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAGGTACACATATACCAATAACTAGCTTATTACATGAACAGTAATGTTTTTTTGGAAGACATA
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaaccc-atattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
||||| | | | |||| | | | | | | || | || | | | || | | |||| | | ||||||||||||||| ||| ||||||||| ||||||||||| ||||
-----gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattattacaatg-----------ttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 6
-tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
| | || || |||||||| | | || |||||| | |||| | | | | |||| | | | | ||| |||||||||||||||| |||||||| |||||||||||||||||
gtaaggacaatctgcactttctgttc--------attatttcgtatca--attaacttgtctaatatcgaaataagttgacatgg-------catttacagTTCATCCAGAAAGCTGGAATCCGATGTGGTCTGTATCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
tgactgtaagc-tattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggat--ttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
|||||| | | || | || | |||| | ||| | ||| | | | | | || | | | | | | | |||||||||||||||| |||||||| |||||||| || |||||
-----gtaagcacagtcttcattttcattcctttgtttattaatttca--atgaacttgtctgttatctaattagctttatcattccatcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 7
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
||||| || | | | ||| | || | | | || || | | |||| || || | || ||||||| |||||||||||||||| ||||| || |||||||||||||||||
-----gtaagtctcttgctgtttcatag-atggaaaatcctttcttatttata-tttagaagttgattttattttcacttttattctgttacttttccagTTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG
upper sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------tgactgt--aagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
| ||| || | || | | || | | || | || || | | | | || | |||| || ||||||||||||| | ||||||||| ||||||||||| |||||
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
ctactttt CT-rich tract
atattacaatttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
- - tgtaagc
- - - - - - - - - tctgttg
- - - - - - - - - - - - - -gcacaaa
- - - - - - - - - - - - - - - - - - - - - - tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - -acccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg