Sequence
atgc intronic sequence ATGC exonic sequencegtaaataatgctcaattatttatttatgccaaatagtcagtcttcattcatataagcatataacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
Basic information
species | Glycine max |
transcript | GLYMA04G38010.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 9
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 8
--gtaaataatgctc---aattatt-tatttatgccaaatagtcagtcttcattcatataagcatataacatttt---aacttgagtt--ttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
|| | ||| || || || | | ||| | || | | | || || | ||| |||| | |||| | | ||||||||| |||||||| ||||| || || ||| |||| ||||||||||| ||||||||| |||||| |||||| | || ||||| || ||||| ||||
gtgtgtcttatgttcccagatgatagtgtctattcatcatgattcacataattgtatgatagtaaatatttttttttcatgttgacctcttcacagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGAAGTCCTTCAGCTGAACGTCGGGTTAATCTGTCAAGCATTA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G136296_T03 (Zea mays), 3'ss of exon 9
-----gtaaataatgctcaattatt-tatttatgccaaatagtca-gtcttcat-tcatataagcatataacattttaacttgagtt--ttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
| | | | || | | | ||| | || ||| | | | | ||| | | | || | |||| | | |||||||| |||||||| ||||| || || ||| |||| ||||||||||| ||||||||| |||||| ||| || | || ||||| || ||||| ||||
gtgtgtcttacattctccgatgacagtgtgtattcatcatgttcacataattgtatgatagtaactattttttttccatgttgatctcttcgcagGTGGTAGAGGTTGTAAGTGGGGATTGCATTATTGTGGCTGATGATTCTGCTCCATATGGCAGTCCTTCAGCCGAACGTCGGGTTAATCTGTCAAGCATTA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 8
gtaaataatgctc------aattatttatttatgccaaat--agtcagtcttcattcatataagcatataacattttaa--cttgagttttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
|||| | | | |||||||| | | || | | | | | | | ||| | | || | || | ||| | | ||||| || |||||||||||||||||||| || |||||||||||||| | | |||||||| ||||| | || || | ||||| || || |||||||| |
gtaagtgctttttctgtgaaattatttgacaaggtcatctctgttaactaaatacttaaatagtcttctatctttacacatcttcctgtctccagGTTGTGGAGGTTGTGAGTGGAGACTGCATCATTGTTGCTGATGATGCTGTCCCATATGGCAGTCCATTGGCAGAACGACGAGTCAATCTCTCAAGTATCAMapped 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|193525790|gb|FK478845.1|FK478845EST: CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAG GTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTG
genomic: CACCGCCTTCAAATTCAAAGGCAATTCATAACCAGAATTTTTCTGGCAAGgtaaataatg ... agttttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatagtcagtcttcattcatataagcatataacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
ttttaac putative branch site (score: 2)
atataagcatataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataatgctcaattatttatttatgccaaatagtcagtcttcattcatataagcatataacattttaacttgagttttacagGTGGTTGAGGTTGTGAGTGGAGACTGTATTGTTGTTGCTGATGATTCCATTCCATATGGTAGTCCTCTAGCTGAGAGGCGAGTTAACCTTTCAAGTATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG