Sequence
atgc intronic sequence ATGC exonic sequence...atattcgacatattgggaataatttatatagttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
Basic information
species | Glycine max |
transcript | GLYMA01G37340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 9
----------------------atattcga--catattgggaat--aatttatatagttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
||| | ||| | | | | ||| | || ||| |||| | | ||||| || | | || | || || | || ||||||||||||||||| ||||| || | ||||||||||||||| ||||| ||| ||||||| ||| | || |||||||| ||||| || |||||||||||
gttcacagaattctcttctgtgtctttcaaatcattctacaagttcatttttctctctctttcttttgaaacaagacatcttcatttcatttaaaatgatttctgaacaacttcttggtggtgtagCAAGGGGAGAAATGGCCATATCCCATACAGAGATTCAAAGCTCACCCGGATACTGCAGTCATCACTGGGAGGCAATGCAAGAACAGCAATCATCTGCACG
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
atattcgacatattgggaataatttatata-gttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
| || ||| |||| || | || | || | | | |||| | || || | ||| | || || |||||| ||||| |||||||| ||||| || | ||||||||||||||| || || ||||| ||||| || || || |||||||| ||||||||||| ||||||||
tggatgaactaattttgaattccttttgcgcgtcgcaattcaactctttgattgcattattaccatccaatttagtctaagctatatgttcatg-ttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 7
-------------------------atattcgacatattggga-ataattt-----atat-agttttattttggaaaggggggttgaat--atttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
| || | | || | |||| |||| ||| || ||| | || | |||| | | | || | | || | | | ||||||||||| |||||||| ||||| |||| ||||||||||||||| || |||||||||||||| || ||||| ||||| || ||||||||||| ||||||||
gtctgttaaggtgctctagccatctgtctttggcggataaaaccacaattccaatcatattagtgctacttttgcaatttgtcttgagccaaatgatacaacaagtgaatctggacaactcatttctgatgcagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTAGGCGGCAACGCGAGAACTGCTATTATCTGCACA
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G338928_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------atattcgacatattgggaataatttatatagttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
|| |||||| | || ||| | |||| | | | || || || | | | | | | | | ||||||||||| |||||||| ||||| |||| ||||||||||||||| || |||||||||||||| || || || |||||||| ||||||||||| ||||||||
gtgcgttaaggtggtctagtcatctgtctttagcagagaaaaccacaatccaaatcatattagtgttacttttgcaatttttctcgaacccccttcaacattacaatttttggacgcctaaatctagacagttcattcttgatgcagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTGGGCGGCAATGCGAGAACTGCTATTATCTGCACG
upper sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 8
--atattcgacatattgggaataatttatatagttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaatt-gcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
|| | | ||| | || ||||||| ||| || | | | ||| || | | | | ||| | || ||| | |||||||| || |||| |||||||||||||| ||||||||||| |||||||||||||||||||||| ||||| |||||||| | |||||||||||| || ||
gaatttccctttcatttcttagtggttgtatagttgaattctgcagctgaaa---ggataattatcaaatctgctagttatataattgggtatttggatgcagCAAAGGAAGAAGTGGACATATTCCTTATAGAGATTCAAAATTAACCCGCATATTGCAGTCCTCCTTAGGAGGCAATGCCAAAACTGCTATCATATGTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
aatatttctttcactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattcgacatattgggaataatttatatagttttattttggaaaggggggttgaatatttctttcactttcatcttaaaaaaaataaaattgcttgcagCAAGGGGAGAAATGGACATATTCCTTTCAGAGATTCAAAGCTAACCCGCATATTGCAGTCCTCATTAGGGGGCAATGCTAGAACTGCTATCATCTGCACC
- - - - - - - - - - - - - - - - - - - - - - -ggggggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa