Sequence
atgc intronic sequence ATGC exonic sequence...cctttagatcttcttccatggttacctcgagacatgtaatttattcttcaaaagtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
Basic information
species | Glycine max |
transcript | GLYMA10G05090.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
cctttagatcttcttccatggttacctcgagac--atgtaatttattcttcaaaagtgcctggtcagaaaatgtgaag-ttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
| || |||||| ||||| | | ||||| ||| | | || | | | ||| ||| | ||| | || | | ||||||||||||||||||| ||||| ||||| |||||||| || ||||||||||| || |||||
--atcttattttcttct-tggttgcagagtttttgatgtatttttatttacagcaaactgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG
upper sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
cctttagatcttcttccatggt-tacctcgagacatgtaatttattcttcaaa-----agtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
|| | || | ||| || | ||| || || | || | | | || | | | ||| || | ||| || ||||||||||| ||||||| ||||| ||||| |||||||| || |||||||||||||| |||||
------tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
upper sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G37500.2 (Arabidopsis thaliana), 3'ss of exon 12
cctttagatcttcttccatggttacctcgagacatgtaatttattcttcaaaagtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
|| | | || | | | || ||| || ||| | || || | | | | ||| ||||| |||||||| ||||| |||||||||||||||||||| |||||||| ||||| ||| | |||
---------------------gtatgt-atgttattttgctatcttcctaacagt---tgttcaagagctg-gacttaacatggagcccatctttttcagGTGATGCAAGGACTTGCTAAATCAATAGCTTGGGATGGTGAAGGTGCTACATGTCTCATCGAG
upper sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 12
cctttagatc--ttcttccatggttacctcgagacatgtaatt-tattcttcaaaagtgcct--ggtcagaaaatgtgaagttttgagttgat-tgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
| || || |||| | ||| | || | || || | || | |||| || || || |||| | | || | | ||| ||||||||||| |||||||| ||||||||||| |||||||||||||| ||||||||||| |||||
-----aagtcagttggctcatgag-gtttagaggcttgaatttctactattatggacagcctttgggtccaatctggtcagttcttaacaaatgtccttttttcagGTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAGMapped 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|16277576|gb|BI942452.1|BI942452EST: CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCG GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACA
genomic: CTTCTCTAGACAGTGATGAGGCTATTCAACTTCAGGCATGCCTAGATGCGgttaagttga ... ttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcaaaagtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
agttgat putative branch site (score: 5)
ttgttctttcc CT-rich tract
agaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttagatcttcttccatggttacctcgagacatgtaatttattcttcaaaagtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - -ccatggt
- - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcctg