Sequence
atgc intronic sequence ATGC exonic sequencegttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
Basic information
species | Glycine max |
transcript | GLYMA07G07540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtc-taagtttgactcttgattctgattttgatgttagtttttttttttaatta--atagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| | | | || || || ||| | |||| ||| | | | | | | ||| || | ||| | ||| | | | | ||| | | | || ||| | || ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | |||| || || | ||| |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|||| ||| | ||||| | || || | || | | |||||| ||| | | | | || | ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
--------------------------------gtgaggattttgtggcgtgtttcggtgatttttct---atgggatttcgatggggattccttgatctgcgtttc--tactggctgttgat----gcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
--gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| || | || ||| || | | ||| | |||| | ||| | || |||||| | | | || | || | | | ||| || | || | | ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcct--gaccgtgttctgcttgctttttttt-----------ttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| |||||| | | | | | || | || | | | | | || | || | | | ||| || | || | | ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
---------------------------------gtctgttttccaattctgcc-tgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
--gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA--------------------
| || | || ||| || | | ||| | |||| | ||| | || |||||| | | | || | || | | | ||| || | || | | ||||||||||| |||||||||||||||||| | || ||||| ||||| || || | || | ||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctgcct--gaccgtgttctgcttgctttttttt-----------ttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| || || | ||||| || || | || | | |||||| ||| | | || | | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
---------------------------------------------gtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcct------gcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
| ||| | || || | ||||| || || | || | | |||||| ||| | | || | | ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | ||| | || | ||| || || || |
---------------------------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcct------gcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgg-gtgtct----aagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|| || ||| |||| || ||| |||||| | | | | | | ||| | || | ||| | | | | | | | |||||||||||||||||||||||| |||||| | |||||||||||| || || |||||| | || |||||||| |||||
-------------------------------------ggattgtgttgtgattac--ttttcttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
gttaatc-caccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattc--tgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|| | || | || | ||| ||| || |||| | |||| | | ||| | | | | || | | ||| | | || | |||| || || | | || | || || || |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | ||||||||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagt--ggctatgaaaaacctctctttcttcgctttcttcctct--ctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA
upper sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gttaatc-caccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
|| | || | || | ||| ||| || |||| | |||| | | | | ||| ||| || ||| | | ||| |||| |||| | || | ||| |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | ||||||||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacct-----ctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttc------cagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAMapped 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|23730924|gb|BU763571.1|BU763571EST: AAGCAAGCGGCGAGAGATGGACTTGATGAAACT GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
genomic: AAGCAAGCGGCGAGAGATGGACTTGATGAAACTgttaatccac ... taattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
EST:
gi|151400703|gb|EV270517.1|EV270517EST: AAAACCATGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACT GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
genomic: AAAACCATGTCTTCTCCAAGCAAGCGGCGAGAGATGGACTTGATGAAACTgttaatccac ... taattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
ttttaat putative branch site (score: 3)
ttagttttttttttt CT-rich tract
attctgattttgatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA