Sequence
atgc intronic sequence ATGC exonic sequence...tatctcttggtttcccaatttgctggatccttctacttcaaccgaaattggcatgtttatccagtttaattattttctaacttgaccaaaatgttttcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
Basic information
species | Glycine max |
transcript | GLYMA11G21600.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G21600.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g72310.1 (Oryza sativa), 3'ss of exon 6
------------------tatctcttggtttcccaatttgctggatccttctactt-caaccgaaattggcatgtttatccagtt-taattattttctaacttgaccaaaatgttt--tcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
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gtaatcttactctctaattgctcttcgattgccgaaataacttgtgacatcatctcgctatcaatgtgtgc-cattgactcattcacgaatgtgttctatttcccccttttcatttgatcagTATGGAGGAGCAAGTTATTAGTCGTGCACATCGTATGGGTGCTACTCGTCCCATATTTGTTGAGACTTTGGCCATGCGTGGTACCATCGAAGAGCAAATG
upper sequence: GLYMA11G21600.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G167668_T01 (Zea mays), 3'ss of exon 1
--tatctcttggtttcccaatttgctggatccttctacttcaaccgaaattggcatgtttatccagtttaattattttctaacttgaccaaaatgttttcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
| | | || | | | | | | || | ||| ||||| | | || | | | || |||| | ||||||||||||| || || |||||||| || ||||| ||||| ||| | ||||| || |||| ||||| || || ||||||||||| |||||||||||||||
ggcagttggtagtcaacacttctaacaagattatttgttatcactgtcattatcatgtatcatctgtg-actgacactcgcactttgtttgt-tacgatcagTATGGAGGAACAGGTTATTAGTCGGGCACATCGAATGGGGGCTACGCGTCCAATACATGTAGAAACTTTGGCTATGCGTGGTACCATTGAAGAGCAAATG
upper sequence: GLYMA11G21600.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G54460.1 (Arabidopsis thaliana), 3'ss of exon 6
tatctcttggtttcccaatttgctggatccttctacttcaaccgaaattggcatgt-ttatccagtttaattattttctaacttgaccaaaatgttttcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
| |||| || | | ||| | ||| | || |||| | ||| || | | | ||| || | || | ||| |||| |||||||| || |||||||||||||| ||||| || || ||||||| ||| ||||| ||| | |||||||| || |||||||| ||||||
tgtctcacggcaacgccttttatattaatattccatatctggtcaaatatttttccattacatggtgttgctgactcctacaatgtttacaa-atgagcagCTTGGAAGAGCAAGTCATCAGTCGTGCTCATCGGATGGGCGCAAAGCGCCCTATTTTTGTAGAAACCTTAACCATGCGTGGCACGATTGAAGAACAAATG
upper sequence: GLYMA11G21600.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g03330.t01 (Vitis vinifera), 3'ss of exon 7
tatctcttggtttcccaatttgctggatccttctacttcaaccgaaattggcatgtttatccagtttaatt-attttctaacttgaccaaaatgtttt--cagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
| || | | | ||||| || || | || || | |||||| ||| | | | || |||| || || | | || ||| ||||| || ||||| || |||||||| || || ||||||||| |||| |||||| ||||||||| |||||||||||||||||||| ||||||||||||
-ctacctgtgctgcaaaatttatatgacatttagagttt--ccttagttggcacatttttactttcaaagagatttactggttttattggtttaacttaccagCATGGAAGAACAAGTGATCAGTCGTGCCCACCGGATGGGTGCTACTCGGCCTATTCGTGTGGAAACTTTAGCAATGCGTGGTACAATCGAAGAGCAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattggcatgtttatccagtttaattattttctaacttgaccaaaatgttttcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
tgttttc CT-rich tract
tttatccagtttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctcttggtttcccaatttgctggatccttctacttcaaccgaaattggcatgtttatccagtttaattattttctaacttgaccaaaatgttttcagTATGGAGGAGCAAGTAATTAGTCGTGCTCATCGTATGGGTGCTTCTCGTCCTATTTATGTGGAAACATTAGCAATGCGTGGTACAATTGAAGAGCAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - -gtttccc
- - - - - - - - - - tgctgga
- - - - - - - - - - - - - - ccttcta
- - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgacc