Sequence
atgc intronic sequence ATGC exonic sequence...aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttgctttctgatttataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
Basic information
species | Glycine max |
transcript | GLYMA19G31730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
aagaaaggggttcaacatacctctactt-ttagaggcattcccatgtcttgctttctgatttataatatataaatcctgtttttcattttaatgctgt--cagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
| ||| | | ||| ||| || || | | ||| || | | || | | | | | | | | |||| |||||||||| ||||| | || ||||||||||| |||||||| || ||||| ||||| || |||||||| || |||||||| || ||||| ||| | | ||
---agttctgtttgaagactgtttacaagttatagttttttctctctctgttcaaggtatatgtcatgttttgagattaataataacccactttctgttccagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
aagaaaggggttcaacatacctcta-cttttagaggcattcccatgtcttgctttctgatttataata-tataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
| | | | | | | ||| | | || || | || || || ||||| | | | ||| | | || | || ||| |||| ||||| ||||| || |||||||||||||| || ||||||||||| |||||||| | ||||| || |||||||| | || || ||| | |||| ||
-gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctg-cagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 2
aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttgctttctgatttataat----atataaatcctgtttttcattttaatgctgtc----agGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
|| | ||||| ||| | | | | | | || | | ||| || || | || || ||| || |||| || | | || | || ||| ||||| || || || || ||||||||||| || |||||||| || |||||| ||| |||||||| |||||||||| ||||| || | | || ||
---aatgaggttcc-----cctatgcatacatattcgttataaccttctgcattaatatagaggatcttgatttaagtcatgttgttaaataccttgttatcttgtagGTATGGTGGCTGCACTAACCAATGAGAGTGCAACCAGCAAATCGGTTTACTTTTCACTTTGCACGTCTGAAATGATATACATCACCCATCTCCTAGCCGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 2
aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttgctttctgatttataatatataa-atcctgtttttcattttaatgctgt-cagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
|| || | | || || | | ||| || || | || | | ||| ||| || || || | ||| | | || |||| ||||| || |||||||| ||||||||||| || |||||||| || |||||| ||| ||||| ||||||||||||| |||||||| | | ||
-agcaaaatttgtacgctatatcgggtagcgcattacatccagtgcctcacggtcagcctaata-tatgtaccatattgctgaacatggtcttatcgtgcagGTATGGTGGCGGCCCTTACGAATGAGAGTGCAACCAGCAAATCAGTATACTTTTCACTTTGCACATCGGAAATGATATACATCACTCATCTTCTAGCACC
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
------aagaaaggggttcaacatacct---ctactt--ttagaggcattcccatgtcttgctttctgatttataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
| || | ||| |||| | ||| ||||||| | | | | | | ||||| |||| | || || || || ||| | ||||||||||| ||||| | ||||| |||||||| ||||||||||| || || ||||| || |||||||| || |||||||| || ||||| ||| || | ||
gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcg----agtaccagttttatcatattt---ctctaattctcttt---atgtt-tcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
upper sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------------------aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttg---ctttctgatt---tataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
| || || | | | ||||| ||| | | || | | | || | ||| | |||| | | | |||||| ||| || | ||||||||||||||||||| || ||||||||||| || |||||||| || ||||||||||| || || || || ||||| || || ||||| |||||||||||
gtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgat-tttccagGAATGGTAGCAGCCCTGACCAATGAGAGTGCTACCAGCAAATCTGTATACTTTGCACATTGTACATCAGAGATGATCTTCATTACTCATTTGTTGGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgctttctgatttataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
ttttaat putative branch site (score: 3)
tgatttataatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaaaggggttcaacatacctctacttttagaggcattcccatgtcttgctttctgatttataatatataaatcctgtttttcattttaatgctgtcagGAATGGTAGCAGCCCTTACAAATGAGAGTGCCACAAGCAAATCCGTGTACTTTGCACACTGCACGTCGGAAATGATATTTATCACTCACTTGTTGGCTGA
- - - - - - - -catacct
- - - - - - - - - - - - - - - - - -cattccc
- - - - - - - - - - - - - - - - - - - - - - - - tgctttc