Sequence
atgc intronic sequence ATGC exonic sequencegtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
Basic information
species | Glycine max |
transcript | GLYMA05G31200.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
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---------------------------------------------------nnnnnnnnnnnnnnnnnnncacattactatttgagtt-ttggta-gctttgttagttcattttcttggagaacagttagcatttcat-tgttcttgctgt-cagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
| | | | || ||||| | | | | || ||| | | | || | | | | | | || | || | ||||||||||| || ||||||||||| || ||||| || ||||| ||||| ||||||||||||||||| || | ||||| ||||| | |
--------------------------------------------------------------------gtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataa-caaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
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---------------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattg---tgtatcaaccatgttcattcttttagttatatgtcattttgaatcatatta-ctgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatg---ttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA-----------
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-------------------------------------------------------------------------gtaagaaatgctgttttttctagggcttctcgcaatgtaatattc--gcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
| || ||| |||| ||| | | | |||| || | ||| ||| | | ||| ||| | ||||| | || | | || |||||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||| || || || |||||||||| |
----------------------------------------------------gattggtttctcaa--attgtttaggtttacatgctgtagatac-ttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgt-taacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
| | | | | | |||| || | | | | | |||| || | | || | | | | | | | |||||||||| ||||| ||||||||||| | ||||| ||||| ||||| || | ||||| ||||||||||| || || ||||| || | |
--------------------------------------------------------tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgcaaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
| | || || | ||| || | | | || | ||||| | || | | ||| ||| | | | | | ||||||||||||||||||||||| ||| ||||||| ||||| ||||| || | ||||| || || || || | || ||||| || | |
----------------------------------------------acaatttttctgtttgggggcagcagagatgaactttac-ctactggtttgtctcctctggcagaccaattgacgttgcttcc---cctgctgaac-----tgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
tgttaac putative branch site (score: 2)
tttattcttacaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA