Sequence
atgc intronic sequence ATGC exonic sequence...tgctgtattccgccttttgctgtatggtggtatacttactgggttcactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
Basic information
species | Glycine max |
transcript | GLYMA14G02110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------------------------------------tgctgtattccgccttttgctgtatggtggtatacttactgggttcact---cctaccttttcttcgta-tttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
|||| | || | | || | | || |||||| | | |||| | | || |||| ||| || | || | |||| || | ||||| || ||||| ||||||||||| ||||| || || || |||||||||||||| || |||||||| |||||||| ||||| || ||||| || |
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatt-tagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
upper sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 5
-tgctgtattcc-gccttttgctgtatggtggtatacttactgggttcactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
| | ||||| | ||| | || | | | ||||| || | | | | | || | ||| | | | |||| |||| ||||| |||||||| || || || || || || ||||||||||||||||| |||||||||||||| || |||||||| || || ||||| || || |
gtacggtatttttgtcttggtttactcggctttgtttcaattgggtatacactgtattataatgcagtcttctcatgtttt------gggggggttttgcagGTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTTGTGGATGATCGCTACACCGGAGAGATTCATGTAACGATAATCGCCACAG
upper sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
----tgctgtattccgccttttgctgtatggtggtatacttactgggttcactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
|| | || | | | | || | | ||| || | | ||| || | ||| | | | | ||| |||| || || ||| |||| |||||||| ||||| || ||||||||||||||||| || || ||||||| |||||||||||| ||||||||||||||||| |
atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttcttgcattttcttatgctaatatttgcatatccatgattc----agGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCGMapped 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|9821132|gb|BE556642.1|BE556642EST: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG GTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTT
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTT
EST:
gi|197664631|gb|FD480334.1|FD480334EST: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAG GTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTT
genomic: TTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaag ... atttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
ccttaac putative branch site (score: 3)
tttttat putative PPT
tgtaatttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctgtattccgccttttgctgtatggtggtatacttactgggttcactcctaccttttcttcgtatttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
tgctgta
- - - - tccgcct
- - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttaac