Sequence
atgc intronic sequence ATGC exonic sequence...attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
Basic information
species | Glycine max |
transcript | GLYMA06G03360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 3'ss of exon 2
attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaaaaatgagcacttttgg-gttaccatttttttt----gtgttaaaaaaact-gtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
|| | | | | | || | | | | ||| || ||| | | || ||| | || ||| | | || | ||||||| | || | ||||| ||||| |||| || ||||| ||||| | || |||||||||||||| |||||||||||||||||||| ||||| |||
------ttattcccattctgcacccatgcattgctcgtagaattcaactgaaggtgattccaccaagcattctcatatcttcctaacaacttatatgatcttgcagGACATTTTGGACTTGGCAAAGTATGCAGCTGTACCTGTCATAAATGGCCTTACGGACTACAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G046748_T02 (Zea mays), 3'ss of exon 3
-attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
|| || | | || || | | || || | || | || | | || | || |||| || || || | ||||||||||| |||| || ||||| ||||| | || ||||| |||||||| |||||||||||||||||||| ||||| |||
cgtttgtccttgttttgatcttgcgtagttccgctcggtgtt-gatccttttttgtttccatccaagcactatctcctaacttctcatatggttttgacagGATATTCTGGACTTGGCAAAATATGCAGCTGTACCTGTCATAAATGGTCTCACCGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 2
attggtttgggaggaatttttatgtgttcaatc-attatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
|| || ||| | | | | || | | | | | | || || | | || | || |||||| || || || | ||||||||||| |||| || ||||| ||||| | || ||||| |||||||| |||||||||||||||||||| ||||| |||
-tttgtccttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTCTGGACTTGGCAAAATATGCATCTGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G157210_T01 (Zea mays), 3'ss of exon 5
attggtttgggaggaatttttatgtgttcaatc-attatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
|| || ||| | | | | || | | | | | | || || | | || | || |||||| || | || | ||||||||||| ||| || ||||| ||||| | || ||||| |||||||| |||||||||||||||||||| ||||| |||
-tttgtccttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTTTGGACTTGGCAAAATATGCATATGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G349547_T01 (Zea mays), 3'ss of exon 2
attggtttgggaggaatttttatgtgttcaatc-attatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
|| ||| ||| | | | | || | | | | | | || || | | || | || |||||| || | | | ||||||||||| || | || ||||| ||||| | || ||||| |||||||| |||||||||||||||||||| ||||| |||
-tttgttcttctcatattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTTTGTACTTGGCAAAATATGCATCTCTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC
upper sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaa---aaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
| ||| | |||| |||| | | | | || || | || | ||| | | | | | | || ||||||| |||||||| || |||||||| ||||| || ||||||||||| ||||||||||||| ||||||||||| ||||||||||||||||| || ||
-gtatgctggtgagttttttaatgtttggtagtactcagatttcaattggtcttgcatatgtgtatttaaagaa--ggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAAMapped 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|21889784|gb|BQ742997.1|BQ742997EST: TTTTGTCTCGCTATAATGACATCATTATGGCTCGTGTTTTTGCTCATAAG GACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTG
genomic: TTTTGTCTCGCTATAATGACATCATTATGGCTCGTGTTTTTGCTCATAAGgtatgctggt ... aaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTG
EST:
gi|192296459|gb|FG989824.1|FG989824EST: TTTGTCTCGCTATAATGACATCATTATGGGCTCGTGTTTTTGCTCATAAG GACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTG
genomic: TTTGTCTCGCTATAATGACATCATTATGG-CTCGTGTTTTTGCTCATAAGgtatgctggt ... aaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
attttttttgtgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaaaaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -ggtttgg
- - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttgg