Sequence
atgc intronic sequence ATGC exonic sequence...aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctggagtttttttatttaaattttaatatatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
Basic information
species | Glycine max |
transcript | GLYMA10G30070.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctggagtttttttatttaaatttta---atatatctgttcatgct-----ctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
| | | | | | | || | | || | | | | | | || ||||| | | | || | || || | || |||||||||||||||||| |||| |||||| |||||||| ||
gtatttttcctcaactaagattttgacatgatccttgcttctctatacattaacaagttgaaccgacaaatctttaacaatttgtcaaactatattattatagctcagccatgtgtaaactcattgcactatctgatgccaatttgttgcacaaacttgaaccaacttcttcctcctcccaacagGTTCATATGGAGAGGTGTACCGTGCTGATTGGAATGGAACA
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 4
-aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctggagtttttttatttaaattttaata-tatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
| ||| || | ||| || | | ||| || || | || | || | | || | ||| || || || || ||||||||||||||||||||| |||| ||||||||||||||| ||
tatgctttttattagtt--gaataggagtgggctggttgcttgaacttgcaccttcctgatctctgcatgaaaactattgattgatttgcttcgttcaatagGTTCATATGGAGAGGTTTACCGTGCTGACTGGAATGGAACC
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------aggct--ccttgtgtgttttga---gtgttgcatgactgtaaatatgtttctggagttttt--ttatttaaattttaatatatctgtt-catg--ctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
| || || ||| |||| || || || | || | || | |||||| ||| | ||| | | | ||| |||| || ||| |||||||||||||||||||| |||| ||||||||||||||| ||
gtacttattttgctaccaagttttgatatacactgtgctgcttttgaactaacaactttgacctgttttggaaactaattttaaatgtgttgaactgtatttcaagttgttagctttgatggacatgttttttattagctgaataggagtgggttggtttcatgaacttgcatttttatagGTTCATATGGAGAGGTTTACCGTGCTGACTGGAATGGAACA
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 5
-aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctggagtttttttatttaaattttaata-tatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
| ||| || | ||| || | | || || || | || | || | | || | ||| || || || || ||||||||||||||||||| | ||| ||||||||||||||| ||
tatgctttttattggtt--gaataggagtgggttggttgcttgaacttgcaccttcctgatctctgcatgaaaactattgattgatttgcttcgttcaatagGTTCATATGGAGAGATTTACTGTGCTGACTGGAATGGAACC
upper sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 4
aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctgga-gtttttttatttaaat--tttaatatatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
|| ||| | | | ||| | | | | || | | | | ||||||| || ||| || | |||||| | |||| | |||||| || ||||||||||| ||||||| ||| |||||||||||
--tcttattggaagaat-ggttgtagtgtttcaatctgagcattgcaatatgctcatttatttggatgttttctgattattattcatgttttgttgtcaatagGCTCGTATGGAGAGGTCTACCATGGTGATTGGAATGGCACAMapped 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|24136021|gb|BU926531.1|BU926531EST: ATGCGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAG GTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
genomic: ATGCGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAGgtaatgatgt ... ttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
EST:
gi|14011342|gb|BG726264.1|BG726264EST: ATGCGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAG GTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
genomic: ATGCGAGATTCCATGGGAGGATCTGGTTCTTGGTGAAAGAATTGGTATAGgtaatgatgt ... ttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggagtttttttatttaaattttaatatatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
ttttaat putative branch site (score: 3)
ctctgtttt putative PPT
tttttttatttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggctccttgtgtgttttgagtgttgcatgactgtaaatatgtttctggagtttttttatttaaattttaatatatctgttcatgctctgttttaaatagGTTCATATGGAGAGGTATACCATGCTGACTGGAATGGCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - tgtgtgt
- - - - - - - - -tgagtgt
- - - - - - - - - - - - -gcatgac
- - - - - - - - - - - - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgctc