Sequence
atgc intronic sequence ATGC exonic sequencegttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
Basic information
species | Glycine max |
transcript | GLYMA07G07540.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaa--gtttgactctt----gattctgattttgatgttagtttttttttttaatta--atagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|||| | | ||| | || | | | | | | |||||| | ||| | ||||| || | | | ||| | | | || ||| | || ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | |||| || || | ||| |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|||| ||| | ||||| | || || | || | | |||||| ||| | | | | || | ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
------------gtgaggattttgtggcgtgtttcggtgatttttct---atgggatttcgatggggattccttgatctgcgtttc--tactggctgttgat----gcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
---gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaat-----taatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| || || ||| || || || |||| | | | || || ||| | ||||| | || || | ||| || || || | ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
gtgaggatgctggacctctcttggtctgtt----ttccaattctgcctgaccg--tgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| |||||| | | | | | || | || | | | | | || | || | | | ||| || | || | | ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
-------------gtctgttttccaattctgcc-tgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
---gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaat-----agGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA--------------------
| || || ||| || || || |||| | | | || || ||| | ||||| | || || | ||| || || || ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
gtgaggatgctggacctctcttggtctgtt----ttccaattctgcctgaccg--tgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| || || | ||||| || || | || | | |||||| ||| | | || | | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
-------------------------gtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcct------gcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| ||| | || || | ||||| || || | || | | |||||| ||| | | || | | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
-------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcct------gcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gttttccttttcccttctatttccattaaagttataattttttttttctaattgg----gtgtctaagtttgactc-ttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|| || ||| |||| || ||| |||||| || | | | | ||| | || | ||| | | | | | | | |||||||||||||||||||||||| |||||| | |||||||||||| || || |||||| | || |||||||| |||||
-----------------ggattgtgttgtgattac--ttttcttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
---------------------gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattc--tgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
||| || |||| | |||| | | ||| | | | | || | | ||| | | || | |||| || || | | || | || || || |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | ||||||||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtg--gctatgaaaaacctctctttcttcgctttcttcctct--ctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA
upper sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
---------gttttccttttcccttctatttccattaaagt-tataattttttttttctaattgggtgtctaagtttgactcttgattc--tgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| | | | ||| ||| | | | | | | | | | || | | ||| | | || | |||| || || | | || | || || || |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | ||||||||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctct--ctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
ttttaat putative branch site (score: 3)
ttagttttttttttt CT-rich tract
attctgattttgatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA