Sequence
atgc intronic sequence ATGC exonic sequence...catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
Basic information
species | Glycine max |
transcript | GLYMA02G04780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA------------
|| ||| | ||| ||| | | || | | || || || | || || | | | | |||| |||| |||||||||||||| || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |
------attgccaatgga---atgaaatgcacccttttttttt-tccagttct--ctgagcttcttttccatcttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgc---agtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
|||| | |||| | ||| ||||| | |||| | | ||| | | || | || || | | | | |||| |||| |||||||||||||| || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |
-ttgtgttacatgat-tgccaatggaatgaaa-tgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
catgtgatctttgatgtatatatgtcatgaaggtatcaccttg-atactgtcctgatgcagtatgggtttatgtttgctgttgatactcat--attttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
| ||| | | |||| || ||| | |||| || || || | | || ||| | | || | || |||| | |||||||||| || |||||||| || || || | ||||| || ||||| || ||||| || ||||| || ||||||||||| |||||||||||||| |||||||| |
tttctgaaatagaacgtatgtaa---atgtttttgtcacttttcatttcatcatctaaaggaatttttttctatatggtactgttactaaatggatttactagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
--catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
||| | || | || | ||| || |||| | | | || | | | || || || || | |||| |||||| || ||||||||||| || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |
tgttgttgaaatagaatccactcatttaatgtttgtgat-cctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA------------
|| | || | ||| || |||| | | | || | | | || || || || | |||| |||||| || ||||||||||| || ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || ||||| ||||| |||||||| |
----------agaatccactcatttaatgtttgtgat-cctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctaggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 3'ss of exon 1
catgtgatctttgatgtatatatg-tcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
| | |||||| | || | | | | | |||| | | || | ||| | | |||||| | ||| ||||| ||||||||||||||||| ||| |||| || | ||||||||| |||||||| || || || || || ||||| |||||||| || || ||||| || |
----------gtaaaccatatataattatagggattgtttttagtccaaattgtgatcccttttgtatacatgat-gttgttga----attgtttgtgtagGTGATAACAAAGTTTTGTTCTGAGAGAATAGCGAGATATGCATTTGAGTATGCGTATCTAAACAATAGGAAGAAAGTGACTGCTGTTCATAAAGCTAACA
upper sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
--------catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctga-tgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
| | || || ||| | ||||||| | | | | | || | | || ||||| |||| || ||| |||| ||||| || |||||||||||||||||| ||||||||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||||||||| |
gaggttaccttcctattctttgc-tatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtat--gtttgtg---gctcatgatgctcat---ttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACAMapped 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|42722520|gb|CK768419.1|CK768419EST: ACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG GTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgtgctctt ... attttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
EST:
gi|15285790|gb|BI469681.1|BI469681EST: ACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAG GTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
genomic: ACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgtgctctt ... attttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
ttttact CT-rich tract
atactcatatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgcagtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
catgtga
- - - - - -tgatgta
- - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - - - - - caccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt