Sequence
atgc intronic sequence ATGC exonic sequencegtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
Basic information
species | Glycine max |
transcript | GLYMA16G04580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgt-ttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
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-----gtctaaccccatcctttttccttttcttttaaaaagtttctg------ctata--atatcacatggtggtgataatagatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 3
gtattattaaggattccagtttctcattaaggttgaatgaagt--attaatgaacctatactgtatgatacattgttttttc----ttattttaactt-tgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
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------------------------------gtttatatatagttcactctggaagttacttaaaaagataccctcttctatggaagttacactaatacatgaccacagGTTGCTTTGAAATTTGAGCACCGAAACAGCAAGGGCTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
||| |||| | || | || || ||| | ||||| ||| | |||| | ||| | | | | |||||| ||| | |||||||||||| | || |||||||| ||||| ||||| |||||||||||||||||||| ||||
gtactattcaaatttttttaaccatatcaaagtt--------ttccaatgattagtcacttca-gatatgctattt------aaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------gtattattaaggattccagtttctcattaaggttg-aatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaacttt---gtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
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gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcga-gtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
|| | || || || | | | | || || || || | |||| | | |||||||| || ||||| ||||| || | |||||||||||||||||| ||||||||||| || ||||| || |||
-------------------------------gtcgg-tggcgt-ttcctcttctttttttgc---ttatgctgattgtg-ttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttc--ttatt--ttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
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------------------------------------gtagactgttcgaagatttgctcagttggattggctcttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
|| | || || || | | | | || || || || | |||| | | |||||||| || ||||| ||||| || | |||||||||||||||||||||||||||||| || ||||| || |||
-------------------------------gtcgg-tggcgt-ttcctcttctttttttgc---ttatgctgattgtg-ttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattt---taactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
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------------------------------------gtagactgttcgaagattttctcagttggattgctcttttctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
ttttaac putative branch site (score: 2)
ctttgttt CT-rich tract
attgttttttcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG