Sequence
atgc intronic sequence ATGC exonic sequencegtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgctttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
Basic information
species | Glycine max |
transcript | GLYMA10G35230.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatg-ctttactgtttcca---tgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
|| | | ||| | |||||| || | | | || | || | | | | | | || | || || || ||||||| | || ||||||||||||||| |||| ||||||| |||||||| ||||||||||| ||||||||||| || | ||||||
---gtcagatcttgtgtga---agttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG
upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
------------gtagtgcaaca-ctatgtaatatagttgtcatataaacaaaataatcatttttttctcatatag-tatgctttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
| | || || |||| || || | || | || | || ||||| | |||| | |||| || || || | | ||||| ||||||||||| |||||||||||| ||||| || || |||||||| ||||||||||| |||||||||||
gtaagagtatatgctctttgccaactgatagatattgtagtta-atggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAG----GACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
--------gtagtgcaacactatg--taatatagttgtcatataaacaaaataatcatttttttct-catatagt--atgctttactgtttccatgaaggatggcactg-actatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
|| | | | | | | || | || | ||| | || || | | | | | ||| | || |||| | |||||||||||||||| ||||||||||| ||||| || || |||||||| ||||||||||| |||||||||||
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG
upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgc--tttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
| | | | | ||| | || | | | | || || || || ||| | |||| ||| | |||| ||||||| | || |||||||||||| || ||||| ||||| ||||| || || |||||||| ||||| |||||| |||||||||||
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattt-tgttgtcactttcattgtccttgcttcttca-gtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG
upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gt-agtgcaacactatgtaatatagttgtc--atataaacaaaataatcatttttttctcatatagtatgc-tttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
|| |||| | ||||| | | | | | | | || ||| | | | || | | |||| | | | | |||||||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| ||||| | |||||||||
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgc-tttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAGMapped 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|7587998|gb|AW703803.1|AW703803EST: GCGGGAAGTTGCTGTCCAG AGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATA
genomic: GCGGGAAGTTGCTGTCCAGgtagtgcaac ... gactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctcatatagtatgctttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
cactgac putative branch site (score: 2)
atatagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgctttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT