Sequence
atgc intronic sequence ATGC exonic sequence...ttcataaatttactgaatgcgtcgatataatcaatatttgatatagttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
Basic information
species | Glycine max |
transcript | GLYMA16G24250.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 9
--------------ttcataaatttactgaatgcgtcgatataatcaatatttgatatagtt-ttgggaaatattttttttcgattttatctaaaaa------tgattaatttgatggcagT-----AAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
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gttcacagaattctcttctgtgtctttcaaatcattctacaagttcatttttctctctctttcttttgaaacaagacatcttcatttcatttaaaatgatttctgaacaacttcttggtggtgtagCAAGGGGAGAAATGGCCATATCCCATACAGAGATTCAAAGCTCACCCGGATACTGCAGTCATCACTGGGAGGCAATGCAAGAACAGCAATCATCTGCACG
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
ttcataaatttac--tgaatgcgtcgatataatcaatatttgatatagttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
| || || | | ||||| | | || ||| | | || | | |||| | | |||| ||||| | | | | |||||||||| |||||||| ||||| || | ||||||||||||||| || || ||| | ||||| || || | ||||||||| | |||||| || ||||||||
tggatgaactaattttgaattccttttgcgcgtcgcaattcaac-tctttgattgcattattaccatccaatttagtctaagc-tatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 7
---------------------------------ttcataaatttactgaatgcgtcgatataatcaatatttg---atatagttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
||||| || | | | |||| | || || | | || ||| | | || | | | | |||| | | | ||||| ||| ||||| |||||||| ||||| |||| ||||||||||||||| || |||||| ||||||| || |||| ||||| || | |||||| || ||||||||
gtctgttaaggtgctctagccatctgtctttggcggataaaaccac-aattccaatcatattagtgctacttttgcaatttgtcttgagccaaatgatacaacaagtgaatctggacaactcatttctgatg-cagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTAGGCGGCAACGCGAGAACTGCTATTATCTGCACA
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G338928_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------ttcataaatttactgaatgcgtcgatataatcaatatttgatatagttttgggaaata-ttttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
|| || || | | ||| | | | || | | ||||| || | ||||| | | | | | | | |||| ||||| |||||||| ||||| |||| ||||||||||||||| || |||||| ||||||| || || | |||||||| | |||||| || ||||||||
gtgcgttaaggtggtctagtcatctgtctttagcagagaaaaccacaatccaaatcatattagtgttacttttgcaatttttctcgaacccccttcaacattacaatttttggacgcctaaatctagaca-gttcattcttgatgcagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTGGGCGGCAATGCGAGAACTGCTATTATCTGCACG
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G51150.1 (Arabidopsis thaliana), 3'ss of exon 10
----ttcataaatttactgaatgcgtcgatataatcaatatttgatatagttttgggaaatattttttttcgattttatctaa--aaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
| | ||||| | | | | || | || || | | | | || |||| | ||| || | || || || ||| |||||| || | |||||| || ||||| ||||||||||||||||| || |||||||| ||| | || || | ||| || || | |||| | || ||||||||
cagtaacgccagtttaccaagt-tattagca-gattgctgtt--attaacatctaatgtttgcttcttttt-acattactgaattatgtggctagcttaatg-cagTAAAGGAAAAAATGGGCACATTCCATTCAGAGATTCAAAGCTGACACGCATACTTCAGACTTCCTTGGGAGGAAACGCCAGAACTTCCATAATCTGCACA
upper sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 8
ttcataaatttactgaatgcgtcgatataatca-atatttga-tatagttttgggaaatattttttttcgattttatctaaaaatgatta---atttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
||||| | || | | ||| |||| | | | || || || | || | | | || ||| ||||| |||| || || |||| |||||||||||||| ||||||||||| ||||||||||| |||||||||| |||| ||||||||| |||||||| ||||| || ||
-----gaatttccctttcatttcttagtggttgtatagttgaattctgcagctgaaaggataattatcaaatctgctagttatataattgggtatttggatgcagCAAAGGAAGAAGTGGACATATTCCTTATAGAGATTCAAAATTAACCCGCATATTGCAGTCCTCCTTAGGAGGCAATGCCAAAACTGCTATCATATGTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
aaatattttttttcga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcataaatttactgaatgcgtcgatataatcaatatttgatatagttttgggaaatattttttttcgattttatctaaaaatgattaatttgatggcagTAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCCTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - -tgaatgc