Sequence
atgc intronic sequence ATGC exonic sequence...catgtgttttaatttgttttacgtgtgaagagtagaattattgcataattaattaattagtttataaattatgttattcattttttgcatcattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGGCTGCCTCTACCTATTGGACTTAAGGCTCCAGCGCTTGATAGTGTGATGA
Basic information
species | Glycine max |
transcript | GLYMA06G44330.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G44330.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G44190.1 (Arabidopsis thaliana), 3'ss of exon 4
-------catgtgttttaatttgttttacgtgtga-agagtagaattattgcataatt--aattaattagtttataaattatg--ttattcatttt-ttgcatcattt------tacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGGCTGCCTCTACCTATTGGACTTAAGGCTCCAGCGCTTGATAGTGTGATGA
|| | |||| ||| || || | ||| | ||||| ||||| || | || ||||||| || | ||| | | || ||| | || | ||||| || ||| ||||||||||||||||||| || ||| |||||||||| |||||||| || ||| | ||||| || | || || |||| |||| ||||
gtgagtgcaccttttttggtttcaattttgtttattagattttgattatgacataacccaaaaaagttttcgaataaattttggataattaacaatatttcattacttgacggttgcagTCGAATGAGAGCATAGATGCAGCTATTGGGGACGTTATATCAAAGCCGTGGCTGCCGCTTCCTTTGGGACTGAAACCGCCGTCGGTTGACGGTGTTATGA
upper sequence: GLYMA06G44330.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g03100.t01 (Vitis vinifera), 3'ss of exon 5
-catgtgttttaatttgttttacgtgtgaagag--tagaattattgcataattaattaattagtttataaattatgttattcattttttgcatcattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGGCTGCCTCTACCTATTGGACTTAAGGCTCCAGCGCTTGATAGTGTGATGA
| | | | | | | | | || | || || ||| ||| | |||| | | || | || | ||||||| || || ||||| || ||| |||||||||||| |||||||||| |||||||||||| |||| |||||| ||| |||| || || |||| | |||||| ||||||||
ggagattgcatggctctctctccatcttaaagggtcagcatgcttgtg-aatagagatattaatccttt--tttttttttctgttttttggtatatattgcagTCCAAAGAGACCATAGATGCAGCCATTGGAGATGCTTTATCAAAGCCATGGCAGCCTCTTCCTCTTGGCCTAAAACCTCCTTCTCTTGATGGTGTGATGGMapped 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|4396303|gb|AI495300.1|AI495300EST: AAGCAGATCACGACATTGGCCTCCCTGGTCCCCTTTTCGACTTTTATCCG TCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGG
genomic: AAGCAGATCACGACATTGGCCTCCCTGGTCCCCTTTTCGACTTTTATCCGgtaaatttct ... cattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGG
EST:
gi|19269844|gb|BM886100.1|BM886100EST: AAGCAGATCACGACATTGGCCTCCCTGGTCCCCTTTTCGACTTTTATCCG TCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGG
genomic: AAGCAGATCACGACATTGGCCTCCCTGGTCCCCTTTTCGACTTTTATCCGgtaaatttct ... cattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattaattaattagtttataaattatgttattcattttttgcatcattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGGCTGCCTCTACCTATTGGACTTAAGGCTCCAGCGCTTGATAGTGTGATGA
aattaat putative branch site (score: 3)
tcatttt putative PPT
aattaattagtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgtgttttaatttgttttacgtgtgaagagtagaattattgcataattaattaattagtttataaattatgttattcattttttgcatcattttacagTCAAAGGAGTGCATAGATGCAGCTATTGGAGATGTTTTATCAAAGCCTTGGCTGCCTCTACCTATTGGACTTAAGGCTCCAGCGCTTGATAGTGTGATGA
catgtgt
- - - - - - - - - - acgtgtg
- - - - - - - - - - - - - - - - - - - - -tgcataa