Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
Basic information
species | Glycine max |
transcript | GLYMA16G33080.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G050186_T06 (Zea mays), 3'ss of exon 10
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggtttctgctgtactaacttatacgatttatcaaataaacca-gACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
| | || | | | || || | | | | | | | ||| || | | | | | ||| ||| | |||| || ||||| ||||||||||| || || ||||||||||| || ||||| |||||||| || || | || ||| |||||||| || | || ||
-----------------------gtactgttcgttaactcattgcaatctgctgtctcctc-ccagtcttcatctaaggtttttcggtttttcttttaaacaaaaaaagACGGCAGGATTCATCTATTGGTTTCGGCGCCCCAGTTCGTGCAAACATGAGGGCTGGTGGCATTTCAAGTGCTCAAGTGACATCATCCTTGTTGGAATCT
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 9
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
| ||| || | | | || || ||| | | | | || ||| | | | | | | | | | | || | || ||| ||||| || |||||||||||||| || || |||||||||||||| || ||||| | ||||| | || | || ||| ||||| || || | || ||
-----tataaattttatcggggtcggctgac--cccaacaaacaccctagatccgcccctgtcttcatctaagttttttttaacttttct-ttcacataaaaaaatagACGGCAGGATTCTTCTATTGGCTTCGGCGCACCAGTTCGTGCAAACATGAGGGTCGGTGGCACTTCAAGTGCTCAAGTGACATCGTCCTTGTTGGAATCG
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggt-ttctgctgtactaacttatacgatttatcaaa-taaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
|| | || || | | || ||| || || | || ||||| | | | | || | | | | ||||||||||||| || || |||||||||||||| || ||||||||||| ||| | ||||| | || | |||| |||| |||||||| || || ||
----------------------gtaattcattattcgtccttttt--tttttttgcaatagattaggggttctgttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacat--atgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
||| | | ||| | | | | | | || | | || | || | ||| | || | | | || | | ||| | | ||||||| ||||||||||| ||||||||||||||||| |||||||| || |||||| ||||||| |||| || ||| || |||||||| ||||| || ||
----tgtgtgtgtgtgtgt-gtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggttttttta-----ccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
upper sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
---gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggt----ttctgctgtactaac------ttatacgattta-------tcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
| | || ||| | || | | | ||| || ||| | ||| | || || ||| || | | || | || | | | ||| |||||||| || ||||||||||||||||| ||||||||||||||| ||| | | | || | || | || |||||||| |||||| |
gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACGMapped 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|24135727|gb|BU926237.1|BU926237EST: TTTATATGTGGTGGAGCATTTATTGATCTTGAAAAAACCATTTCGGAGAG ACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAG
genomic: TTTATATGTGGTGGAGCATTTATTGATCTTGAAAAAACCATTTCGGAGAGgtaatgttgg ... aataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAG
EST:
gi|16276814|gb|BI942058.1|BI942058EST: TTATATGTGGTGGAGCNATT-ATTGATCTTGAAAAAACCATTTCGGAGAG ACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAG
genomic: TTATATGTGGTGGAGC-ATTTATTGATCTTGAAAAAACCATTTCGGAGAGgtaatgttgg ... aataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatatgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
tactaac putative branch site (score: 0)
ttatacgatttatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG