Sequence
atgc intronic sequence ATGC exonic sequence...tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatc-tgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||| | | | | ||| || | | ||| || | || || ||| ||| ||| || || ||| | ||| | | |||| |||||||||||||| || || || ||||| |||||||||||||| ||||||||||| || || || ||||| ||||| ||||| |||||||||| |
--gtatatatacaggagcaacctgttagaactaaaac----atatttcagtacaagtcttt--tcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttacta---tctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||| | | | | ||| || | | ||| || | || || ||| ||| ||| || || ||| | |||| | | |||| |||||||||||||| || || || ||||| |||||||||||||| ||||||||||| || || || ||||| ||||| ||||| |||||||||| |
--gtatatatacaggaccaacctgttagaactaaaac----atatttcagtacaagtcttt--tcttatctagattttttctaacacccttttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
---------tagtagcaaaatactaaaaacaagtgacagaaaa-acttttgattgctttgtctaaccttttgaccttgtctgaatacttactatctg-ttttatattga-----agGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||| |||| | | | || | || | |||| | |||| | | ||| || | | | || | |||||| |||| |||| |||| ||||| ||||| || || || |||||||| || || ||||||||||||||||||||||| |||| ||||||||||| | ||| | || |||||||
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctca-tatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
---------tagtagcaaaatactaaaaacaagtgacagaaaaact-tttgattgctttg--tctaaccttttgacc----ttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||| |||| | |||| || | | | | || || || || | |||| | | ||| | || | ||| | || | ||| || | | |||| ||||| ||||| || || || |||||||| || || ||||||||||||||||||||||| |||| ||||||||||| | ||| | || |||||||
gtatacaagtaggagcaca-tacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgct-tttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
------tagtagcaaaatactaaaaacaagtgacagaaaaacttt---tgattgctttgtcta-accttttgaccttgtctga-atacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||||| | | | | | | |||| | ||||| || | | | | | ||||| |||| | || | | |||| | | |||| || || |||| || || || |||||||| ||||||||||||||||||| |||||| || |||| ||||||||||| | ||| | || |||||||
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgttt---agGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------tagtagcaaaatactaaaaacaagtgacagaaaaacttttgat-tgctttgtctaaccttttgaccttgtctga-atacttac--------tatctgttttatattga---agGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
| || | |||| | | | | | | | ||| | | |||||| | | | | || | ||| ||| || || ||| | | | || |||| ||||| | || || || || |||||||| ||||||||||||||||||| |||||| || |||| ||||||||||| | ||| | || |||||||
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttat-tgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
tagtagcaaaatactaaaaacaagtgacagaaaaactttt---gattgctttgt--ctaaccttt--tgacct-----tgtctga-atacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
| | | | || | || | || || |||| | || ||| | | | ||| ||| || ||||||| || | | | ||| || | | |||| ||||| ||||| || || || |||||||| ||||| ||||||||||||| |||||| || |||| ||||||||||| | ||| | || |||||||
-----gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgat-tttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
tagtagcaaaatactaaaaacaagtgacagaaaaactt--ttgattgctttgtctaaccttttgaccttgtctgaatacttact-atct-----gttttat-attgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
||| | | | | | | | || || | || || | | || | | | ||| ||||| || | |||| |||||| ||| |||||||||||||||| || || || || || || |||||||| |||||||| ||||| ||||||||||| ||||||||||| || |||||||| |||||||
---------aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
| || || || | || | | | | | ||| || | ||||||| | | | ||||||||||||||||||| || || || ||||| ||||| || ||| | ||| ||||||| || ||||||||||| ||||| | ||| | || || ||||
-----------------------------gtaaggct----atagtttctggttatactctatctttggttgg-----tctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgtctaaccttttgaccttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
tacttac putative branch site (score: 1)
tctgtttt putative PPT
tatctgttttatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - aaaacaa
- - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatctg