Sequence
atgc intronic sequence ATGC exonic sequence...ttgtccctttttttctacctacacacttcgaagatgattcctaacctttttagcttcctgtacattgctgatatctatgcacctagtttacaattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
Basic information
species | Glycine max |
transcript | GLYMA09G02960.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
-------------------------------------------------------------------------------ttgtccctttttt-tctacctacacacttcgaagatgattcctaacctttttagcttcctgtacattgctgatatctatgcacctagtt-tacaattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
||| | || | || || | | ||||| | ||| || || | || | | | | | | |||||| || ||| ||||||| |||||||||||||||||||||||||| || |||||||||||||||| |||||| ||| || ||| ||| | ||||||||||| || |
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgc-taaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------ttgtccctttttttctacctacacacttcgaaga-----tgatt-cctaacctttttagctt---cctgtacattgctgatatct-atgcacctagtttacaattttc-----agGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
|| | |||| ||| | || || || | ||| | | |||| | ||| | | || | || || | || | ||| |||| |||| |||||||| ||||||||||| ||||||||||| ||| || ||| |||| ||||| || || || | || ||| | ||||||||| | || |
gtatttccatgaaaaagttgcaattttcaacataacatatcgggatgagtttgtgtctgccttatttgtttaattcagacctacagagagcggctaacttgtacatttctttttttggtttctctgcagGCGGAGCATGGTCCAGATAGTCAAGTTGTTCTTGTAGTTGTGGGCGATAGTGTAGATCTCAACGCCATCGAAGAAGAAATTGCCAAGCAGTGCAAAAGCC
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 12
ttgtccctttttttctacctacacacttcgaagatgattcctaacctttttagcttc---ctgtacattgctg-atatctatgcacctagtttaca-attttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
|| | |||| | | || | | | || ||| | | | ||| | | | | | || || | || || |||| ||||| ||||||||||| |||||||||||||||||||| |||||||| ||||| ||||| || | || || |||||||| ||||||||||||| | || |
-----cccctatttccatatgcatgtgtaaagcaaagtttttaagttctctgctttcaattttcatactatttcatccctgatgtttcaattgacttatttccagGCTGAGCATGGCCCTGATAGTCAGGTTGTTCTTGTAATTGCTGGGGATGGCGTGGACCTAAGGGCTATTGAGGAGGAAATCAGCAAGCAGTGCCAAAGCC
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S15_472V6.1 (Physcomitrella patens), 3'ss of exon 11
ttgtccctttttttctacctac-acacttcgaagatgattcctaacctttttagcttcctgtacattgctgatatctatgcacctagtttacaatttt-cagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
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--gtgtaatcagcgatagtttctatacgttgaatccattaccagattggtcatattttcgctgttctggttatgtaattttgttctgtttggtatattgcagGCAGAACATGGGCCAGATAGTCAGGTGGTTCTTGTAGCAGCAAGTGATGAAGTAGACATCGCTGCCATACAGCACGAGGTGGAGAGACAATGTAGGGATTMapped 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|23056573|gb|BU577749.1|BU577749EST: CAGACAAGCATGCAATTCCTTCCCATGTAGCTGCTGATTTGCTTTCCCAG GCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGT
genomic: CAGACAAGCATGCAATTCCTTCCCATGTAGCTGCTGATTTGCTTTCCCAGgtttaataag ... caattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttagcttcctgtacattgctgatatctatgcacctagtttacaattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
tgctgat putative branch site (score: 3)
ttttc putative PPT
tagtttacaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtccctttttttctacctacacacttcgaagatgattcctaacctttttagcttcctgtacattgctgatatctatgcacctagtttacaattttcagGCAGAGCATGGCCCAGATAGTCAGGTTGTTCTTGTGATTGCTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGTGACAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-tgtccct
- - - - - - - - - -tacacac
- - - - - - - - - - - - - - - - - tgattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacct