Sequence
atgc intronic sequence ATGC exonic sequencegtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA
Basic information
species | Glycine max |
transcript | GLYMA11G03420.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 8
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------
||| || | | | || | || || || | || || || | |||||||| | |||| ||||||||| || || |||||||| || ||||| |||||||| ||| ||||||||||||||||
---------------------------------gtatgcgcaaagcatataattcgcctattgttagttttt-tgtagtgcaaagcctaacgt--actatttgatgatttgttaa-gGAGAAGCTTCCACCAACGGATTCAAGACTCAGGCCAGATCAGCGGCATCTAGAGAATGGGGAGTACGAAAAGGCTAACTCTGAAAAATTGCGCCTGGAGA
upper sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 8
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------
| || | | ||| | | || | | || | || || | || | | | | || | | ||||||||||| || || |||||||| ||||| ||||||||||||||| | || |||||||||||
---------------------gtacacatgg-aacatacatatatcccataatctgagttctgttagctcttaacc-taaaaggctacgacacatcttttacgctcttg---ttaagGAGAAGCTGCCACCGACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGA
upper sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------
| || | | || || | || || || | ||| || | | | || | | | | | | |||| ||||||||| || || |||||||| ||||| |||||||||||||| | || |||||||||||
---------------------gtacacatgg-aacataaatataacccatcat---tggacttccgttagttcttaacctataatgctaaggc-acatttctacccttttgttaa-gGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
upper sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 8
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGT--ATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------
| | || || ||| || | || || |||| || | | || || ||||| || ||||||| | || | ||||| | |||| |||||| || || ||||| || || ||||||||||||||||||||| |||| |||||||| |||
----------gtatgttcag--atggtttaatcttgttt-ttattctgtttatggattgctatactatcttttcatatagacttgtctgatcttgtgttaacttgatgatggat-gtagGAGATACTTCCTCCCACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAA
upper sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 7
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------
||| | || ||||||| |||| | ||| || | |||| ||| | | ||||| | ||||||||| ||||||||| | |||||||||||||||||||||||||||||| |||||||||||| ||||||||||| || || |||||||||||||| ||||||||||||| |||
gtaga-gataatgtattgaatcaatttttttatgtgcatattcattttcctct-tatgcatatctaattgtcttttatagctctgtctgatcccgggtatttgatcacggattaa-gGAGAAGCTCCCACCCACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGAMapped 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|9259271|gb|BE347479.1|BE347479EST: ATTTGACACCATTTGCCATCACTCTGAATGAGCTTACTCCGGGACTGAAG CTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCC
genomic: ATTTGACACCATTTGCCATCACTCTGAATGAGCTTACTCCGGGACTGAAGgtatataatg ... ttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA
ctctaat putative branch site (score: 3)
taattgttgtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA