Sequence
atgc intronic sequence ATGC exonic sequence...attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
Basic information
species | Glycine max |
transcript | GLYMA14G37510.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
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------gtatatata-caggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
attgggaaatgtagaac--attggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| || || || | | | || | | ||| | | ||| | || || ||| ||| | |||| | |||| || || | |||| ||||||||||| || || ||||| | || |||||||||||||| || |||||||| || || || ||||| ||||| || |||||||||||||| |
--gtatatatacaggaccaacctgttagaactaaaacatatttcagt-acaagtcttttcttatctagatttt---ttctaacaccctttttt-ttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
--------attgggaaatgta------gaacattggcaacaagtgccagatag---actgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| || | || | || | | | ||| |||| | | || | | || | | || | || | | | || || | | ||| || | |||| ||||| |||||||| || ||||||| || || || ||||||||||| ||||||||||| |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgt--atttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
--------attgggaaatgta---gaacattggcaacaagtgccagatagactgttga--ttagtttgttattttctgttgtttgactgctaattctctt-tattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| || | || | ||| ||| | | | | | || || | ||| ||| || ||| | || || |||| || | |||| ||||| |||||||| || ||||||| || || || ||||||||||| ||||||||||| |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
--------attgggaaatgta---gaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgac-tgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| || || || ||| | ||| | | | || | | | | | || | | | | |||| | | ||| ||| || || |||| || || ||||||| || ||||||| || ||||||||||||||||| | |||||| || |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtt-tctatgatatatttctttctgacatacctgctcttttttttgttt---agGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
----attgggaaatgtagaacattggcaacaagtgccagatagactgttgattag---tttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| | | | | | ||| || | | || | | | | | | | || | | ||| |||| | | | |||| || | |||| ||||| |||||||| || ||||||| || ||||| ||||||||||| | |||||| || |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------attgggaaat-gtagaacattggcaacaagtgccagatagactgttgatt---agtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
|| || | | || ||| | | || | || ||| | || ||| | | || || | | || | || || | |||| ||||| | ||||| || ||||||| || ||||||||||||||||| | |||||| || |||| ||||||||||| |||||||| || ||||| |
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctg----ttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| || | |||| ||| | | || || || | | | | | | || | ||||| || | |||| ||| | ||||||||||||||||||| || ||||| | ||| |||||||| |||||||||||||| ||||||||||| |||||||||||| | ||| |||| ||||| |
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatatt--ttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
attgggaaatgtagaacattggcaacaagtg-ccagatagactgttgattagtttgttattttctgttgtttga---ctgctaattctctttattattatgaa--------gGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
|| ||||| | | ||| |||| | | ||| ||| | || | | | || | || | | | || || |||| |||||| |||||||||||||| ||||| | ||| ||||| ||||| ||||| |||| ||||| || || ||||| ||||| ||||| ||||||| || |
------------ggagtattggattctctggtccaagtagagtatgcattgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
tgctaat putative branch site (score: 2)
ttctctttattatt CT-rich tract
taattctctttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - -aatgtag
- - - - - - - - - - - - -caagtgc
- - - - - - - - - - - - - - - - - - - -actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgc