Sequence
atgc intronic sequence ATGC exonic sequence...tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
Basic information
species | Glycine max |
transcript | GLYMA07G03820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 2
tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgt-----ccttacaattgctcatggaatgg--acagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
|| ||| | ||||| | | ||| | | | | ||| || | | | ||| | || | | || || || | ||||| | ||||||||||||| || ||||| |||||| ||||||||||| || ||| || |||||||| |||||||||||||| || | || | | |
-----ttatcttgtctcatccttctggataggt--tctacagtatgttcttctatatggtggtcaagtttcttgaaaaccatgtattttcttattattttcttacagAGTAGCGATGCTGAAGAAGGCAAGTCCAAGAAGGGGCAATATGAAGGACCAGATATGGACTTGGCTGCCATGCTTGAAAGGGATGTCCTGGATTCTACCC
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 2
tgccctttgcttattgcatcccttagtctagatagtttgagaaac-gtttaacttctta-gatat-gtggttgtgt--ccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
|||| || || || | | | | || || | | ||||| | |||| || ||| ||| | || | | | ||| | | |||||||| || |||||||| |||||| |||||||||||| || ||| || || |||||||||||||||||||| || | || | |||
-----attgccacttatatttttttgcgggcaaattgccagctactgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttttttctagAGTAGTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTC
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054715_T02 (Zea mays), 3'ss of exon 1
tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC-----
| | || |||| | | || || ||| | | ||| || | | | | | | || | | ||| | | |||||||| || |||||||| |||||| |||||||||||| || ||| || || |||||||||||||||||||| || | || | |||
cacttatatttttttgcgggcaaattgccagcta--ctgactggcttctaatgataaagtttttgaaaaatcttccttttccaattcttt---tttctagagtagTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAATATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTCCAGGA
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 2
tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgt----ccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
|||| || | | | | || | | | || | ||||| | || || ||| || | | | |||| | | |||||||| || |||||||| |||||| ||| |||||||| || ||| || || |||||||||||||||||||| || | || | |||
----aattgccagttatttttttgtgagcaaattgccagttactgaattgcttctaatgatatttttttttgaaaaatcttctttttccaactctgttttccagAGTAGTGATGCTGAGGAAGGTAAGTCCAAGAAGGGTCAGTATGAAGGGCCAGATATGGACTTAGCTGCAATGCTTGAAAGGGATGTTCTGGATTCTACTC
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 2
tgccctttgcttattgcatcccttagtctagatagtttgagaaa-cgtttaacttcttagatatgtggttgtgtccttacaa--ttgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
|| | || | | |||| | || ||| | | ||| || | | || || | | | ||| | | ||| | || ||| | ||||||| |||||||||||||| || ||||||| | | || ||||| || ||||||||||| ||||||||||||||||||||||| || || || || |
-accttcactttgtaagaaataatagtg-atgtaacttgtgtgttcatttgacct-tcagttagtcaatattctgcttcctaatttgtttgtgtaattgctagAATGGTGATGCTGAAGATGGAAAATCAAAGAGGGCACAGTATGAGGGACCTGATCCAGACTTGGCTGCAATGCTTGAAAGGGATGTTTTGGAGACTAGCCMapped 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|209725769|gb|BW659900.1|BW659900EST: CTGCTTCTGGAAAGGCTAGCAAGACGGATGCCGCTGCTGCAGCTGTAACT AATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCT
genomic: CTGCTTCTGGAAAGGCTAGCAAGACGGATGCCGCTGCTGCAGCTGTAACTgtaagtttca ... gaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaacttcttagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
tccttac putative branch site (score: 2)
ttagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgccctttgcttattgcatcccttagtctagatagtttgagaaacgtttaacttcttagatatgtggttgtgtccttacaattgctcatggaatggacagAATGGCGATGCTGAAGATGGTAAGTCAAAGAAGCCTCAATATGAAGGTCCTGATCCAGAATTGGCTGCAATGCTTGAAAGGGACGTGTTAGAAACCTCTC
tgccctt
- - - -tgcttat
- - - - - - - -gcatccc
- - - - - - - - - - - - - - - - - - - gagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaca