Sequence
atgc intronic sequence ATGC exonic sequence...tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgcattgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
Basic information
species | Glycine max |
transcript | GLYMA19G43630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 2
tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgttt---atgcattgaatgtgaatgtgc--agTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
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-gtatgtttcaattaacatttccattctattaaagtatgttgttcctccatttcatttcatt-tttgttcattgttttaaatgtttttttttttggttttcccagTCGTTTATCTCGATGCTGATACTGTGGTCGTGAAAAGTATTGAGGATCTTTTCAAGTGTGGGAAGTTCTGTGGCAACCTGAAGCATTCTGAAAGAATGAA
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 2
-tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgc--attgaatg-tgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
| ||||| | |||| ||| | | | | ||| | | | | | | || ||| || | | || ||||| || | | |||||||||||||||| || || ||||| || || |||| ||| || ||||||||||||||||| || || |||| || || ||||||||||| || ||||
gtatgcttttcagtt-atttttctagttcatcgttatatgtctc-tgtatcatggcctttactttgtttttgttcattgttctaatagaatgctgcctttccagTTGTTTACCTTGACGCAGATACTATAGTTGTGAAAAGTATCGAGGATCTTTTCAAGTGTGGCAAGTTTTGTGGAAACTTGAAGCATTCTGAAAGAATGAA
upper sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
-----tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgcattgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
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tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattatt-----gttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|213620033|gb|DB965367.1|DB965367EST: GGGTGTCTACACAAAGCTCAAAATATTTAACATGACTGACTACAAGAAAG TTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTT
genomic: GGGTGTCTACACAAAGCTCAAAATATTTAACATGACTGACTACAAGAAAGgtaacatttt ... gaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTT
EST:
gi|213606612|gb|DB972533.1|DB972533EST: GGGTGTCTACACAAAGCTCAAAATATTTAACATGACTGACTACAAGAAAG TTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTT
genomic: GGGTGTCTACACAAAGCTCAAAATATTTAACATGACTGACTACAAGAAAGgtaacatttt ... gaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcggtacaatgtgtggtttattggttgtttatgcattgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
ttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgcattgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-ggaggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt