Sequence
atgc intronic sequence ATGC exonic sequence...atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
Basic information
species | Glycine max |
transcript | GLYMA10G30930.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
-------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
|| |||| ||||||| | || | || || || | || || || | || | | | | || | || | ||||| ||||| || || | ||||||||||| || |||| | | |||| |||||||||| ||||||||||||||||| |||||||| |||||||| |||
ttgcctattgagttttgccttacagtggct--ttaatattgtagtatattttacaactaattat---gttactgtattc--attgaacatatgaaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaag-tacgagctgacttgaaaatgtcactat-tagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
| || ||| || ||| ||| | || | || | | | | ||| | | | || || ||| | || | | | || ||||||||||||||| |||||||||| |||||||||| | || |||| || |||||||| ||||| |||||||| | ||| | |||||||||||||| |||
--------gtgagaatggtgaatgtttt-catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 8
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcact-attagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
|||| ||| |||| | || | | | ||||||||| | | ||||| | || | |||||| ||||||||||| ||||||| |||||| || |||| | ||||| ||||||| |||||||| ||||| |||||| | ||||| |||||||| |||
----------gtaagttgtg-atataagggtccgaaagttgcagacagatacgattttaagtcttt------ttatctgacacaagtatacgttggactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaa----agtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
| ||||| | | | || | || || | |||| | ||| | | | |||| | | | | |||| | | | | |||||||| || | || ||||| | |||| || ||||| ||||| |||||| |||||||||||||||| | ||||||||||| |||||||| ||
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgat--gcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttc-tggtttttaagtcatcaaagtacgagct---gacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
|| || ||| | | | ||| | | || | | || | | | | ||| | ||| | || | | || | ||||||||||| |||| ||||| | | || | | | | ||||| |||||| |||||| ||||||||| | ||||||||||| |||||||| ||
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgat--gcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
|| ||| || | | || |||| | ||| | | | ||| | ||| | || || | ||||||| | |||||||||||||| | ||||| ||| | |||| || | || |||||| |||| | |||||||||||||||||| ||||| |||||||| ||||| |||
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatcta---acaagtgg---tgaaaat---aaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
upper sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
|| ||| | || | | | |||| ||| | |||| | | | ||| |||||||| || || ||| ||||| | | ||||| | || || || |||| | ||||||||||||||||||||||| ||||| ||| | || |||
---------------------------------gtaagcgacgtcttgaatcttctgtaag--atcga----tcgattgac---agatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAAMapped 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|58019797|gb|CX706539.1|CX706539EST: TCTTGAGTACTG GTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCT-ACNAAGGAATGAAC
genomic: TCTTGAGTACTGgtatttattt ... tcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAAC-AAGGAATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
agctgac putative branch site (score: 3)
tttttaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA