Sequence
atgc intronic sequence ATGC exonic sequence...tgaggtttcctcctttactttttgaaattatcttgaggtttactaccctactgttccatgttttggagtttgcattgactagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
Basic information
species | Glycine max |
transcript | GLYMA19G05360.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------tgaggttt---cctcctttactttttgaaattatcttgaggtt-------tactaccctactgttc---catgttttggagtttgcattgactagacattatacctattg--cagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
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gtacctataacaattgtgaaagaactgcttgccctgatttttgttgaatgttccctattattttttaactttctgttgtcttagtagttatttctaaattatcaggatattgtcttaagagtcatacatatcttgtcaacattattacatttctatactattttttggacagACACTGGTCATATACGAGACATCTGCATCAGAATTGGAAATAATTCGTGACATATCACGTACTTTTCCATCACATATTTTCTTCCAACAGAGACATGGTC
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 3
-tgaggtttcctcctttactttttgaaattatcttgaggtttactaccctactgttccatgttttggagtttgcattgactagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
|| || | ||| | | || | | || | | | || || | || || | | | ||| | |||| ||| || |||||||||||||| ||||||||| |||| || ||||| || || || || || || || || ||| ||||||||||||| || ||||| |
ttgcatttatatttcttaataaacagagttctatgtagactagtgttctcgttattg-atatattaaccttatttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 3
tgaggtttcctcctttactttttgaaattatctt-gaggtttactaccctactgttccatgttttggagtt-tgcattgactagacatta--tacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
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--------------------------gtaatcttcgccgtttatatccttacattgtttcttctctgagtcatattctgatcatctatcgattttcctatgaagCAATTGGTGATTTATGAAACATCTGCATCAGAGCTTGATATCATTCGAGACATATCCCGTACTTTCCCATCACATGTTTTCTTTCAGAAGAGACATGGAC
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 3
tgaggtttcctcctttactttttgaaattatcttgaggtttactaccctactgttccatgttttggagtttgca-ttgactagacattatacct-attgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
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--gtaataacttattatctccttgtg--tgttttgttattcattttctttggcttcattgctggaaagaaaaaaacttacaattctctcgatttcattatagCAACTGGTGATTTATGAGACGTCGGCATCAGAACTCGATATCATTCGGGATATATCTCGTACTTTCCCGTCACATGTTTTCTTCCAGAAGAGACATGGAC
upper sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 3
tgaggtttcctcctttactttttgaaattatcttgaggttt---actaccctactgttccatgttttgga-gtttgcattg----actagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
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-------tttttcgtagatttctgatgatcctttgatatttgggagttcctttcagatagattctcttcatattcttattgtgctgatgaaaaatgtacttgtc-cagCAACTGGTAATATACGAGACATCTGCTTCAGAATTGGATATAATTCGAGATATTTCTCGTACCTTCCCATCACATGTTTTCTTCCAGCAGAGACATGGACMapped 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|151405260|gb|EV275074.1|EV275074EST: TGATATCTGGAAGTCGAGACCTATTGCTGATGAACCCTGGAGTTTATGAG CAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGAT
genomic: TGATATCTGGAAGTCGAGACCTATTGCTGATGAACCCTGGAGTTTATGAGgtaattaact ... cctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctactgttccatgttttggagtttgcattgactagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
cattgac putative branch site (score: 3)
acattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaggtttcctcctttactttttgaaattatcttgaggtttactaccctactgttccatgttttggagtttgcattgactagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattg