Sequence
atgc intronic sequence ATGC exonic sequence...gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
Basic information
species | Glycine max |
transcript | GLYMA07G15170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
--gaaaagaacggctagtatga-tattcaaaagttcttccattgacattgtcat-caaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
| | | || ||| | | | ||| | || | | | | || | | | | | || || | | ||| || |||||| || ||||||||||||||||| |||||||||||||| |||
tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgt----tatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 9
-gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaa-acttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
| | || | ||| | | ||| | |||| | | || | | | || ||| | || | | | | | |||||| |||||||||||||||||||| |||||||| ||||||||
attcacatattcctcatgtgaatccatgatgaatttctaacttttttgttttagttatttcattatactgtccttattccttttctatggtacct--tgcagGGTTTATTGCAATGTATGCTACTCTTGCAAGCAGAGACGTG-----------------------------------------------------------
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 9
------------------gaaaagaacggctagtatgatattcaaaagt-------tcttccattgacattgtcatcaaacttgact-ttgcttcatatatgctttattttgg-atttat-----gatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
|| ||| ||| | | |||| | | ||| || | | | || ||| || | | || | | ||| | || | || ||||||||||||||||| ||||||||||| |||||||| |||| |||
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAAGCAGAGATGTG-----------------------------------------------------------
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatatatgctttattttggatttatgatgcagGATT-TATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
| | | || | || | ||| | | || || | | | | ||| | | ||| |||| |||| | ||| | ||| | || | |||| | | || | | | |||| | | || ||| |
--gtaagtttccctgcatacaaactgaagaatgttc-----atgctttctcaaagcgtag--tagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTAT----GCTACTCTTGCAA--------------------------
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G132069_T01 (Zea mays), 3'ss of exon 8
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatat-atgctttat-tttggatttatgatgcagGATTTATTGCAATGTATG--CTACACTTGCAAGTCGAGACGT--GGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA-----------------------------------------
|| | || || | ||||| | ||| | | | | | | |||| | | || |||| || | | | | | | | | ||||||||||||||| || ||||| ||||| ||||||||||| | || || ||| |||
----------------------------------------------gtacgtacgctctgct--gattcatcttatgttcgacgtgagaaaagaagatgttgagccaaatgaaatgagtgaccgcttccttctgcttgctgcctcagGACTGTTGCTTAATCCCGGAGTCGCCCTTCTACCTTGAAGGGAAGGGAGGGCTCCTTGAGTTTGTCGAGAGACGGCTCAAGGACAACGGACACATGGTCA
upper sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 9
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcat-caaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
|| | || | |||| | ||| | || | | || || | ||||| | || | || |||||||| || |||||| |||||||||||| ||||||| || || || ||||| |||||||||||||| |||||||| ||||||||||| |||||||| | |||||||| | |||
-cttgtcactgacagagctgtccattttctttctcctatttatgtttctgttctaagtttgcattgctctctctacaatctaaattggatttgtggtgcagGGTTTATTGCAATGCATGCTACCCTGGCCAGCCGAGATGTGGACTGTTGCTTGATTCCAGAATCACCCTTTTATCTTGAAGGGCCAGGTGGACTTTTTGAMapped 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|33390216|gb|CA853423.1|CA853423EST: AAGTGTTGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCG GATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCT
genomic: AAGTGTTGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCGgtaagtttcc ... tatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCT
EST:
gi|7591258|gb|AW706995.1|AW706995EST: AAGTGTTGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCG GATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCT
genomic: AAGTGTTGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCGgtaagtttcc ... tatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatcaaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
acttgac putative branch site (score: 4)
atatatgctttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatatatgctttattttggatttatgatgcagGATTTATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA