Sequence
atgc intronic sequence ATGC exonic sequence...acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
Basic information
species | Glycine max |
transcript | GLYMA03G36050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g34000.1 (Oryza sativa), 3'ss of exon 6
acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtt-tttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| ||| || || | | |||| ||| || | |||| || ||| | || || || | ||| |||||| || || || || ||||| || | |||||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| | ||||| |||||||||
gtgagtatcattttagcaagctgctaaaatgaaccctcattctctggcttatcatttacta--tttattgacaatggccttttttcttttcttaattttagGTATAAGGTTTTCATTAATCCAAGTGTCAGTGATGTTCTATGCACAGCGACAGCTGAGGCTCTTGCAATGGGGAAATTTGTTATCTGTGCAGATCATCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
---acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| | | | | | | | |||| | || |||| || | | | |||| || | || | || ||| | || || |||||||| || ||||||||||| |||||||||||||| || ||||| || || |||||||| | || ||||| || ||||| || || || || || |||
gtaaaagacagagcctctcactgcctgacatcttcctac---atct----ttagatatagttaatttgaatgtttttcctg-----ttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: AC233887.1_FGT006 (Zea mays), 3'ss of exon 6
------acacatgattctttctcatcctttacatgcccagactca-atctggaatttgtttttattaagtt--tggttcttat-tttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| || | | | | | | | ||| |||| || |||| | || || || ||| | | || | | | || |||||||| || ||| | ||||| || |||||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||||| |||||||||
gtgaggttctacgaagcatcaaagctactaaaacgacatcacttttatcttgatcttgtcctatgcaaattgctgattcaggtatctgttttcttctgttgaattttcagGTACAAGGTTTTTGTCAATCCAAGTGTTAGTGATGTGCTATGCACAGCAACAGCTGAGGCCCTTGCAATGGGGAAATTTGTAGTCTGTGCAGATCATCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
---------acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacac----tttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| ||| || |||| || || | | ||| | ||| ||| || ||| | || || || || ||| | || || |||||||| || || |||||||| |||||||||||||| || |||||||| || || ||||| ||||| ||||| ||||| || | || || || ||||||
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataa--ttaattctgtattccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G100766_T01 (Zea mays), 3'ss of exon 1
acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttatt---gtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| ||| || |||| || || | | | | |||| | | |||| || ||| | || || || || | | |||| ||||||||| || || | |||||| |||||||||||||| ||||||||| | ||||| |||| ||||| ||||| ||||| || | || || || ||||||
aaacaagaaactttaaggcaattgtcaaagata-attaattctgtattccacttttttt--gttgattactaatgctgccatttgctgtttgtatttttttagGTACAAGGTTTTCAAAAATCCGAGCATTAGTGATGTCCTATGCACAACAACAGCATAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G002043_T02 (Zea mays), 3'ss of exon 8
---------acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgt---agGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| ||| || |||| || || | | ||| | | |||| ||| || ||| | || || || || | | |||| | |||| ||| || || | |||||| |||||||||||||| || |||||| | ||||| ||||| ||||| ||||| ||||| || | || || || ||||||
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataa--ttaattttgtatttcactttttt--gttgattactgatgctgccatttgctgtttgtattttttcagGTGCAAGGTTTTCAAAAATCCGAGCATTAGTGATGTCCTGTGCACAACAACAGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| | | | | | | | || || | | |||| | |||| ||| | | ||| || ||||||||||| || ||||| || ||||| || ||||| ||||||||||| || || || || || |||||||| || ||||| || ||||| ||||| ||
---------------gtaagttctgaaaaatgtgctttgcttttaaa---aacttgttaaggtttcgctctttgattgtctttcccacatcttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT
upper sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 6
--acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
| ||| | || | | | | || || | || || || ||| | || || | ||| || | | ||| || ||||||||||| |||||||| || | ||||||||||| |||||||||||||||||||| ||||| ||||| || |||||| | ||||| || || |||
gactgaaatatttctcctggggaataatgtagttccatataaat--gattgtgaacaaatgaaccttgctgattgttgtcacatctttctttttccttgcagTTACAAAGTCTTCATAAATCCCAGTGTCAGTGATGTGCTCTGCACAGCTACAGCTGAGGCCCTTGCTATGGGTAAGTTTGTAATATGTGCAGACCACCCAMapped 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|208170482|gb|GD969717.1|GD969717EST: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCATGG GTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTG
genomic: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCATGGgtaggaacac ... cttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTG
EST:
gi|16997085|gb|BM086457.1|BM086457EST: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCATGG GTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCT
genomic: AATCTCAACTTTCAGAAAGGAAGAGATCATGCAGACGATTCTCTTCATGGgtaggaacac ... cttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
ttttgac putative branch site (score: 3)
ctttatcctt putative PPT
tttttattaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacactttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-cacatga
- - - - - - - ctcatcc
- - - - - - - - - - - - -catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacacac