Sequence
atgc intronic sequence ATGC exonic sequencegtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
Basic information
species | Glycine max |
transcript | GLYMA13G36570.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 8
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgagagataat-tactaatgtg-ttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
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gt-attgcatgatgttgtgcaagctacattttttt-------ttttgccacgggtatttcttgtgttaacttgatattatggcagGTTCTTGGTACTCCAACCCGTGAGGAAATACGATGCATGAACCCCAACTATACTGAGTTCAAATTTCCTCAGATTAAGGCTCATCCTTGGCACAAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 8
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgaga-gataattac--taatgtgtttt-cttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
|| | |||||| | | | | || || | | | | | ||| | ||||| | | | ||||| ||||||| ||||| ||||| || || || |||||||||||||| || ||||| || ||||| || || || || || |||||||| ||||| |||
----------gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgaga-gataattac--taatgtg-ttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG----
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----------gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
|||| ||| | || | || || ||| | | | | |||| | ||| | |||||| | ||| ||||||| ||||| || || |||||||| || |||||||| || || || ||||| ||||||||||| || |||||||| || ||||||||||||
gtgaactcttcttttattatattttgttttggcgtcatttcctgtctgtgctcat-gatg-----tgctgtgttggtt--tagGTTCTTGGTACTCCAACTCGCGAAGAAATCCGGTGCATGAACCCAAACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
| || ||||||||| || | | | || | ||| | | | | | || ||| |||||| || ||||||| ||||| || || |||||||||||||| ||||| || || || |||||||| || ||||| || ||||||||||| |||||||| |||
gtgaagtctcctttattagactaatggatgtgctcttttttgtctttggtatta--gactagaatctagtaaatatgttaccataagtacacttgctaccttgtttt-----agGTTCTTGGTACTCCAACTCGTGAAGAAATTCGATGTATGAACCCGAACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
gtgattccttgtct-ttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
||| | | | | ||||| || ||| | |||| || | | || | |||| | ||| |||||| ||| ||||||| ||||| || |||||||||||||||| ||||| || |||||||| |||||||| || || || |||||||||||||||||||| |||
gtgcagcatcatttcttgttgatattatcgaggatcatctgc-tatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAGMapped 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|17402010|gb|BM178792.1|BM178792EST: CTTTGTTCCCAGGAGAAAATCAGGTCGATCAACTCGTGGAAATTATCAAG ATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTAT
genomic: CTTTGTTCCCAGGAGAAAATCAGGTCGATCAACTCGTGGAAATTATCAAGgtgattcctt ... tttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTAT
EST:
gi|298181881|gb|HO026056.1|HO026056EST: CTTTGTTCCCAGGAGAGAATCAGGTCGATCAACTCGTGGAAATTATCAAG ATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTAT
genomic: CTTTGTTCCCAGGAGAAAATCAGGTCGATCAACTCGTGGAAATTATCAAGgtgattcctt ... tttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
tactaat putative branch site (score: 1)
tgttttctt CT-rich tract
agataattactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA