Sequence
atgc intronic sequence ATGC exonic sequence...tcttttaatatctggaccagtatctgttacacattttcatgcacatttgtggggttgtggtccagcgtatgataatgagtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
Basic information
species | Glycine max |
transcript | GLYMA15G05080.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
tcttttaatatctggaccagtatctgttacacattttcatgcacat--ttgtggggttgtggtccagcgtatgataatg-agtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
| ||||| || || | | | || | |||| ||| | | || | | | | | ||| | || || ||| ||||||||| | ||| | ||||||||| ||||||| || ||||| || |||||||||||| |||| |||||||| || |||||||| || | || |
-catttaacatttgcaac--tttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
upper sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
tcttttaatatctggaccagtatctgttacacattttcatgcacatt-tgtggggttgtggtccagcgtatgataatgagtgtgttca---ttgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG--------
|| | || | |||| | | | || || || | | || | | | | ||| | | | | | | || |||||| || ||| | ||||| ||| |||||||||| |||||||| ||||||||||| |||| ||||| || || |||||||| ||| | || |
---gcgggtagcatgaat-gcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
upper sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
tcttttaatatctggaccagtatctgttacacattttcatgcacatt-tgtggggttgtggtccagcgtatgataatgagtgtgttca---ttgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
|| | || | |||| | | | || || || | | || | | | | ||| | | | | | | || |||||| || ||| | ||||| ||| |||||||||| |||||||| ||||||||||| |||| ||||| || || |||||||| ||| | || |
---gcgggtagcatgaat-gcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG
upper sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------------------tcttttaatatctgg-accagtatctgttacacattttcatgcacatttgtggggttgtggtccagcgta-tgataatgagtg--tgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
|| | || ||| | || | ||| | | ||| | || | || || | | | |||| | | | | || |||||||||| | ||||||||||| ||||||||||| || || ||||| |||||||| ||| |||| ||||| || ||||||||||| ||||| || |
gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG
upper sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
-----tcttttaatatctggaccagtatctgttacacattttcatgcacatttgtggggttgtggtccagcgtatgataatgagtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
| ||| || || ||| | | | || | || || || | | ||| ||| | ||| | | |||||| || | || || |||| ||| |||||||||||||||||||||| || |||||| ||| |||||||| || |||||||||||| | ||||
gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcg---agcaccctttgtacttgccat--tttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtggggttgtggtccagcgtatgataatgagtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
ttgtaac putative branch site (score: 2)
tatgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttaatatctggaccagtatctgttacacattttcatgcacatttgtggggttgtggtccagcgtatgataatgagtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG
- - - - - - - - - - - -ctgttac
- - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtg