Sequence
atgc intronic sequence ATGC exonic sequence...tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G32930.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 6
tgattttcccatccgccccaat-cctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
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---gtgagcaatctattttagtacttctactattatttacaacttccttatttttcttctactttactg-----------atgcatccaa-----atgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G031609_T02 (Zea mays), 3'ss of exon 6
tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| | |||| || | || | || | || |||| || | | | | ||| | ||| || | | | ||| |||||||| | || |||||||||||||| |||||||||||||||||||| ||||| || ||||||
--------gtaagcattccaa--cttcataacc--tttaattttcccctttttgatatttttttagttaataatgatatatggttg-tggattt---cagCTCAAAGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 6
-tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| | | ||| | | | | || | | | | | | || ||| | ||||| || || ||| || |||| || ||| ||| | || |||||||||||||| |||||||||||||||||||| ||||| || ||||||
gtaagcattccaactttc----ttccctttaattttcctgtttttatatatttttgaagttaataatgaaaacatggttgtgaatttc-----------agCCCAAGGGATGTGCTGATGCGTGTTGTGGCCCAAAATCTTTCTCCTGAGTTAACTCTAGTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 6
tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| || || ||||| | | | | | | | | |||| | | ||| | || | || || || || ||||| ||||| || ||||| |||||||||||| | |||||| |||| |||||||||||||| || ||||||
--------------gtaagcattctatgttagtaaaacagtattgtcca--tgatccctttctaactgttgg-tgttgtataatt---atgttc-tgcagCTCAAAAGATATACTTATGCGTGTTGTGTCACAAAATATTTCCCCTGAGTTGACTCTAGTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G131118_T01 (Zea mays), 3'ss of exon 4
-tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| | | ||||| || || | | || |||| | || || ||| | ||||| || || ||| || | ||| || |||||||| | || |||||||||||||| |||||| ||||||||||||| ||||| || ||||||
gtaagcattccatct-tcctaacctttaatt-----tcccctttttgatattttttag-ttaataatgatat-atggttgtggatttt-----------agCTCAAAGGATGTGCTGATGCGTGTTGTGGCCCAAAATATTTCTCCTGAGTTAACTCTTGTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177485_T01 (Zea mays), 3'ss of exon 1
tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| | |||| || | | || |||| |||| || | | | | ||| | ||| || | | | ||| |||||||| | | |||| ||||||||| |||||| ||||||||||||| ||||| | ||||||
--------gtaagcattccaacttcctaaccttta----atttttccctttttgatatttttttagttaataatgatatatggttg-tggattt---cagCTCAAAGGATGTGTTGATGCATGTTGTGGCCCAAAATATTTCTCCTGAGTTAACTCTATTAGAAAAG
upper sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
| ||||| ||| || || | || | | | || | | || | || | | || ||| | | |||| | | |||||||||||||| || || ||||| |||||||| ||||| |||||||||||||||||||| |||||||||
gtattattcatttctctactggctcctatcttttctgactgtaactttgtatcaacaaggttttatttttgcattagcagcatt--tcaggaggtgttttgatgtctgtttatatctac--tggtggttactt-atgtctgtttgtttcaactaacttgcagTTCAAAGGATATTCTTATGCGGGTTGTGGCACAAAACCTTTCTCCTGAGTTGACTCTGGTGGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
ttaatgttttctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgattttcccatccgccccaatcctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG
- - tttccca
- - - - - - ccgcccc
- - - - - - - - - - -tcctctg
- - - - - - - - - - - - - - - - -catccca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctt