Sequence
atgc intronic sequence ATGC exonic sequence...gtcatagactacttgaaattgtattgccaactttagttaagctatttttatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
Basic information
species | Glycine max |
transcript | GLYMA08G16780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
----gtcatagactacttgaaattgtattgccaactttagttaagctatttttatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
||| | | | || || || | ||| ||| || || |||||||||| | | ||| |||| || |||| || |||||||||||| ||||||||| ||||| || || || ||||| |||||||| |||||||| || |||||||| | ||
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagt--cgccaacttacttta--cccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
---gtcatagactacttgaaattgtattgccaactttagttaagctatttt-tatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
| || | |||| ||||| | | || | || || | | ||| || | | | || | | |||| || |||| || |||| || |||||||||||| ||| ||||| ||||| || || || ||||| |||||||| |||||||| || |||||||| | ||
cgggacagacgtaacttag---tgtatcattagttatattatagatacaatgtttgcatactagcctttttatcatgcgtaatcgccaacttattttaccc-agGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
gtcatagactacttgaaattg--tattgccaactttagttaagctatttttatgcggtcttgtaat-atcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG---------------
|| || | | | | ||| |||| | | || | || | | | |||| | | ||| | | | | ||| | |||| || |||||||||||| |||||| || ||||| || || || ||||| |||||||| || ||||||||||| ||||| | ||
gttttaccgttcctagggctaatggttggaggtcactgttattgtgtgggtac-taaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G135816_T01 (Zea mays), 3'ss of exon 5
gtcatagactacttgaaattg--tattgccaactttagttaagctatttttatgcggtcttgtaat-atcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
|| || | | | | ||| |||| | | || | || | | | |||| | | ||| | | | | ||| | |||| || |||||||||||| |||||| || ||||| || || || ||||| |||||||| || ||||||||||| ||||| | ||
gttttaccgttcctagggctaatggttggaggtcactgttattgtgtgggtac-taaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtcatagactacttgaaattgtattgccaactttag--ttaagctatttttatgcggtcttgtaatatcatgtttcttaatgttgcctttctttt--gtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
| | ||| | | | |||| || || | | | || | |||||| || | |||| | | || ||||| | | |||| ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| ||||
ggccaagatcatt----gccctgaaattcacttcagctttcaagtgtccttgtctggtctttgcctaatacgtttttcatatttcttgttcttgttggctgcagGTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAGMapped 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|21595390|gb|BQ610465.1|BQ610465EST: TGAGACGTGGTGCAGAGGATGATGAACTTAGAGAGATAATAGCGGCAGCA GTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACT
genomic: TGAGACGTGGTGCAGAGGATGATGAACTTAGAGAGATAATAGCGGCAGCAgtatgcactt ... tttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
tcttaat putative branch site (score: 3)
ttgcctttcttttgtc CT-rich tract
ttgtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatagactacttgaaattgtattgccaactttagttaagctatttttatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - ctacttg
- - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt