Sequence
atgc intronic sequence ATGC exonic sequence...ttgtctcatttgtagatattagaaaaggttcacctttgattttttaagatttagttaatatttgaggaagcttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
Basic information
species | Glycine max |
transcript | GLYMA13G16560.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 9
ttgtctcatttgtagatattagaaaaggttcacctttg--attttttaagatttagttaatatttgaggaagcttat---cattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
|| | | ||| || ||||| | | ||| || || | | | || | | |||| |||| || || | | | ||||| ||||| | || ||||| || | ||||||||||||||||||||| |||| ||||||||||||||||| ||||||||
--gttttggat-caga-atgggaaaaacataagttttaccataaccagagttcaacctttcatctcatactgcttccgtgcatttttgttccttttctg-tacagGTTGAATATTCTTGCTGAGCTCCTCTGTTTTGGTGATCGTGAATTCTACAAGGACTGGTGGAATGCCAAAACAGTTGAAGAG
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------------ttgtctcatttgtagatattagaaaaggttcacct----ttgattttttaagatttagttaatatttgaggaagcttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
| | |||| | || | | | | || | || | || || | | | | |||| || | | | ||||||| |||| | || ||| |||||||||||||||| |||||||||||| | |||||||||||||| ||||| |||| ||
gtaatttccattttctacttattcataatcaagaaaatggtcactattagactataatatattcaaaatcaatttatttctgaatgcatacatttccttgcatgatccaagcttgtgaacaaataatttctctaacaccagacttacagtttaaacattgataattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G169089_T01 (Zea mays), 3'ss of exon 9
--------------------------------------ttgtctcatttgtagatat-tagaaaaggttcacc----tttgattt-tttaaga-tttagttaatatttgaggaagc-ttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
|| || | | | | | || || ||||| | ||||| | | || ||| || |||| || || | || | || | ||| | || || | || || || || | || ||||| ||||||||||| |||| ||||||||||||||||||||||||||
gttagtatcttgcttcagttcaacagtaccttaaatttgtgcggcagtgattggtttatataacaggttaattgggttttgacctgcatgggactttgatttccattttccatggcattcttgtttgctcttttggttggtttcagGCTGAACATTGTAGCTGAACTCCTCTGTTTCGGTGACCGTGAATTCTATAAGGACTGGTGGAATGCCAAAACTGTTGAAGAG
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G130749_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------------------------ttgtctcatttgtagatattagaaaaggttcacctttgattttttaagatttagttaatatttgaggaagcttatcattggagtgactgtcgta-atgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
| | | || | | | | | | | | ||||| | | | || | ||||| | | | | | | | || | || |||||||| ||| | || ||| |||||||||||||||| || ||||||||| | || ||||||||||| || || |||| ||
gtagtaaattatattttctatctattcattcaaattcaaatacatgatcgatcctgatattattctaatatcagtcatcgatgcttcttctccgaacatgcatgctctcggagaaaattatttcc----ttttatgctct--ttcaaatttgcatatttgcagtttcgaacttatattcatctatacagGTTAAACATACTTGCTGAGATTCTTCGATTTGGTGACCGAGAATTCTACAAAGACTGGTGGAATGCAAAGACAATTGATGAG
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------------------ttgtctcatttgtagatattagaaaaggttcacct---------ttgattttttaagatttagttaatatttgaggaagctt--atcattgga-gtgactgtcgtaat-gtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
|| | ||| | | | | ||| | | | || ||||| |||| || || | | ||| | | || | | || | | | | || | |||||||| ||||||||||||||||| | || || ||||||||||||||| | |||||||||||||| |||| ||| | ||||
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
upper sequence: GLYMA13G16560.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g01930.t01 (Vitis vinifera), 3'ss of exon 9
ttgtctcatttgtagatattagaaaaggt-tcacctttgattttttaagatttagttaatatttgaggaagcttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
| || ||| ||| || | | | |||| |||| | || ||| || | | || |||| || | || ||||||||||||| | || ||||||||||| ||||| || ||||| ||||| | |||||||||||||| ||||| ||||| ||
taaaaatataaacagagtttaccaattctattatctttcatttgtctgaatcatattactaagacatatcatacttagatgcagtg-ttgcaattatatagGTTAAATATACTTGCTGAGCTTCTTCGTTTTGGGGACCGTGAGTTCTATAAAGATTGGTGGAATGCAAAAACAGTTGAGGAGMapped 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|192302397|gb|FG996679.1|FG996679EST: CCAAATTTATATGTGTGGCTCTGCATGTTCTATTGCTTTTTCCACCTTTG GTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCA
genomic: CCAAATTTATATGTGTGGCTCTGCATGTTCTATTGCTTTTTCCACCTTTGgtattccatc ... cgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCA
EST:
gi|27809171|gb|CB063593.1|CB063593EST: CCAAATTTATATGTGTGGCTCTGCATGTTCTATTGCTTTTTCCACCTTTG GTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTG
genomic: CCAAATTTATATGTGTGGCTCTGCATGTTCTATTGCTTTTTCCACCTTTGgtattccatc ... cgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatttagttaatatttgaggaagcttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
agttaat putative branch site (score: 4)
ttagttaatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtctcatttgtagatattagaaaaggttcacctttgattttttaagatttagttaatatttgaggaagcttatcattggagtgactgtcgtaatgtagGTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - -acctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg