Sequence
atgc intronic sequence ATGC exonic sequence...tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcatacatgatattcttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
Basic information
species | Glycine max |
transcript | GLYMA16G30180.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30180.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g13540.1 (Oryza sativa), 3'ss of exon 4
tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcataca--tgatattcttggat---atattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
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----gatgcgtagaatattgaatcttccaatgataacaacatttttggtagttcg-actattggatacagttagcattaactaattctatttttctatttgacagTATGTCCCACAACCATGAAACGCATCTGCAGGCAACATGGGATTTCTCGTTGGCCATCTCGAAAAATTAACAAGGTCAACCGGTCTCTCTCAAAACTAAA
upper sequence: GLYMA16G30180.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G475305_T01 (Zea mays), 3'ss of exon 4
--tcagaaaacacaaaattggtcattatctattactagtagct-ttcgtttttattagtagcagctcatacatgatattcttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
||| ||| | | ||| | | | | || || | || | | || || | | ||| | | || | | ||||||| ||||| || ||||||||||| || ||||||||||||| || ||||||||||||||||| || || ||||| |||| || || || || || ||
gagtagaggcggcaacacagtggattttgcagtggtgtaagtggttgactcttggagattgtgagcattaactggtgtactt---tttcttggttcctggcagTTTGTCCTACAACTATGAAGCGCATTTGCCGGCAGCATGGGATTTCTCGTTGGCCATCTCGAAAAATCAATAAGGTCAACCGATCTCTCTCGAAACTAAA
upper sequence: GLYMA16G30180.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G176655_T01 (Zea mays), 3'ss of exon 4
--tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcatacatg-atattcttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
| | | || | | | | | | | || | | || | || || ||||||| || || || |||||| || ||||| |||||||||||||| |||||||| ||||| || || || |||||||||||| | || | |||||||||| | | | || || | ||
cattcatgtgtttatatttatttgatttgagtccattcatgtcatgattgggaaaaaagaaagtcgacacttggatattctaaatcatgtttttt---tacagTATGTCCTACAACAATGAAGCGCATTTGTAGGCAACATGGTATTTCTCGCTGGCCATCTCGACAAATCAGCAAGGTTAACCGTACTGTTTCAAAATTAAA
upper sequence: GLYMA16G30180.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G375675_T01 (Zea mays), 3'ss of exon 4
tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcatacatgatattc---ttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
| | || ||| | | || | | || | | || | | || | | || | || | | || | ||||||| ||||| || ||||| |||||||| |||||||||| || || |||||||||||||| || || || ||||| ||| || || || || | ||
---ggcagcaaaaagcggatttttcagtggtgataacgatgtaaggggttgactcttggagattgtgagcattaattagtttcactttttttatatctggcagTTTGTCCTACAACCATGAAACGCATCTGCCGGCAGCATGGAATTTCTCGTTGGCCATCTCGGAAAATTAATAAGGTCAACAGGTCTCTCTCGAAATTAAA
upper sequence: GLYMA16G30180.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02070.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcatacatgatattcttggatatattcttgctgt-------acagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
| |||| | |||| ||| ||||| | | | | || | | | | ||||| | | | || |||| | ||||||||| | |||||||||||||||||||||||||| || || ||||||||||| || || || ||||||||||| ||||| || |||||||| | |||||| || ||||| ||
gtacgtttctacacttaaaaaagttgtttgcaatcttgctctgttatttccaaaatgctgaattaatca---tctat-agaaatcggattgttctattgcaatagcaattgaaatgaattaatcttatcaagattcttgcttttacatttacagTTTGCCCTACTACAATGAAGCGTATATGCAGGCAGCATGGAATCTCCCGGTGGCCATCTCGTAAGATCAACAAGGTTAATCGTTCCCTCTCTAAGCTAAAMapped 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|13311569|gb|BG405229.1|BG405229EST: GCAACATTACTTCACAGGAAGCCTTAAGGATGCTGCAAAGAGCCTTGGTG TTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTT
genomic: GCAACATTACTTCACAGGAAGCCTTAAGGATGCTGCAAAGAGCCTTGGTGgtatgctatg ... tgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttattagtagcagctcatacatgatattcttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
ttcttgct CT-rich tract
atatattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagaaaacacaaaattggtcattatctattactagtagctttcgtttttattagtagcagctcatacatgatattcttggatatattcttgctgtacagTTTGCCCTACTACAATGAAGCGCATCTGTAGGCAGCATGGGATATCACGTTGGCCATCTCGAAAGATAAAAAAGGTTAACCATTCCCTGTCCAAGCTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - -acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catacat