Sequence
atgc intronic sequence ATGC exonic sequence...tattgtttcttccatccaagtggagtcatcttcctcttcctcctcttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
Basic information
species | Glycine max |
transcript | GLYMA17G34020.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
-------tattgtttcttccatccaagtggagtcatcttcctcttcct----cctcttattctcatctttgtcatcttctt----tgacctgctttta--cctttgcctacatt-cagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
| ||| | || | | || | | || | | ||||||| | | | | || || ||| | | || | | ||| || |||| ||||||||||| | ||||||||||| | ||||| ||||| || |||||| |||||| || ||||||||||| || ||||| ||||| | ||||| || |
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
tattgtttcttccatccaagtggagtcatc---ttcctcttcctcctctt----attctcatct-ttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
|| ||| || | | || || || || | | | || ||| | | || | || || | ||| ||||| |||| | |||||||||||| | ||||||||||| | ||||| |||| ||| | |||| ||||| |||||||||||||| || ||||||||||| | ||||| || |
---tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttttaatgttttctgatttgctt--ggtattgctc---tgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G180575_T01 (Zea mays), 3'ss of exon 6
tattgtttcttccatccaagtggagtcatc---ttcct---cttcctcctcttattctca--tctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
|| ||| || || | || || || || | | | || | | | | || || | || || | ||| ||||| |||| | |||||||||||| | ||||||||||| | ||||| |||| ||| | |||| ||||| |||||||||||||| || ||||||||||| | ||||| || |
---tgaatctatcacataaactgcgttgtcaagttactaaacatacatttcaaaatttgagttcgttttaatgttttctgatttgctt--ggtattgctc---tgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
--tattgtttcttccatccaagtggagtc---atcttcctcttcctcctcttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
| | ||| | | | || || |||| | | ||||| | || | || | ||| | || || || | | ||||| ||||| ||||||||||| || ||||||||| | ||| | |||||||||||| ||||||| ||||||||||| || || || || ||||||| || |
gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctctt----ctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
------tattgtttcttccatccaagtggagtcatcttcctcttcctcctcttattctcatctttgtcatcttctt--tgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
| |||||| ||| | || | | | || | || | || | |||| || || |||| | || | ||||||| ||||| ||||||||||| || ||||||||||| ||| | ||||||| || | |||||||||||||| || ||||| ||||| | ||||| || |
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtgttcctgttctcactgttttgatttttgcgctga-tgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
upper sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 6
---tattgtttcttccatccaagtggagtcatcttcctcttcctcctcttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
|| || | || || ||| || | | | | | || | || | || | | || | |||| | | | ||| ||||| ||||||||||||||||| || ||||||||| ||||| | || |||||||||||||| || ||||||||||||||||| || || |||||||||||||
ttaaccaagtttaataattggtgaaaagccaacttgct--tgttgcccctgttaaggttattatgat-tcttatggtttttttttctcatctctgccatacagGAAAGTGATGTGAAGTGGGCATCTAGATGGGATACCTATCTTCTCATGAGTGATGACCAGATCCACTGGTTCTCAATTGTTAATTCTTTGATGATTGTTCMapped 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|193360960|gb|FK323840.1|FK323840EST: AAGAGAACCAGGAAATTATCTTCACATATGATGTTGATTTCCAG GAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGT
genomic: AAGAGAACCAGGAAATTATCTTCACATATGATGTTGATTTCCAGgtgaggttat ... ctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
ctttgac putative branch site (score: 4)
cttttacctttgcct putative PPT
tttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattgtttcttccatccaagtggagtcatcttcctcttcctcctcttattctcatctttgtcatcttctttgacctgcttttacctttgcctacattcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC
- - - - - tccatcc
- - - - - - - - - -gtggagt
- - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttgc