Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
Basic information
species | Glycine max |
transcript | GLYMA02G47860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaat-ataggaaaaggatattaaacttgttctggtt-----attgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
||| | | ||||| | ||| |||| || |||| ||| | ||| | |||||| | || |||||| ||||| |||| |||||| |||| ||| |||| |||||| ||||||| || ||||| ||||||||||||||||||| || || ||| | |||||
--------gttacagttcatgaggcagcc-tttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA
upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatatta----aacttgttctggttat-----------tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
|||| || ||| ||| | ||| | |||| | || | | | | || | || |||| | | || ||| ||| | ||||||| | ||| |||| |||||| |||||||| | || |||||| |||||||||||||||| |||||||||||||| |||| || |||||| | |||||
----gtttgaatcgaattta--tctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA
upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 4
---------------gtttgtttat---tataaaattaattctatttgtt--tctttgtattttg----tttaaaaaatatagg-aaaaggatattaa------acttgttctggttat----tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
| | | || | || |||| || || ||| | || |||| |||| | | || | ||| | ||| | | || ||| | ||||||| | ||| | || |||||| ||||| | | || |||||| |||||||||| ||||| |||||||||||||| |||| || |||||| | |||||
gtctgaagctaattcatctatccatgtttgtataattgat-ctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA
upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 2
---gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggata---ttaaacttgttctggttat-tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
| | | | | | | | || | | | | | | | | ||| | | ||| ||||||| | ||| |||| |||||| |||||| | | || |||||| |||||||||| ||||| |||||||||||||| |||| || |||||| | |||||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctgctcacaggtcgcagaagtgacagattatctgatcatgctcaggcttttctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA
upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 4
--gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaactt---gttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
| | ||| || | | || || | || || | | | | || || || || ||| | ||||| |||||||| ||||||| || ||||||||||| || || | | |||||| |||||||| |||||||||||||||||||||||||||| || || ||||| || ||
gtgccactctatcatcaga--aacagcatcttttcctctttccccaaaactgacactaaagtgtaatatcatggttcttttaatgctggtaattgcagCAACAATGCTCGCAGCACAGAGTATCCAGTTGGGTGTCAATGATATTGTTGTGTCTGGTGGTATGGAAAGCATGTCTAATGTGCCTAAATACCTAGCAGAMapped 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|298197389|gb|HO044868.1|HO044868EST: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAG CTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
genomic: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtttgtttat ... gttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
EST:
gi|298168588|gb|HO009518.1|HO009518EST: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCACCAGGAATGAAAG CTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
genomic: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtttgtttat ... gttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
tttaaaaaatatagga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG