Sequence
atgc intronic sequence ATGC exonic sequenceTCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaatatttagtctattgataacatgttgtggttttgtgggtgtaattggagataatgtatcccatt...
Basic information
species | Glycine max |
transcript | GLYMA04G01240.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 5'ss of exon 9
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaa---ttattgaagcatttgctt---tagacttaaatatttagtct-attgataacatgttgtggttttgtgggtgtaattggagataatgtatcccatt
|| || || |||||||| || |||||||| ||||| || || |||||||| || |||||||| ||| | ||| |||||| |||||||||||||||||| |||||| | || || || | || | ||| | || || |||||| |||| | | | || | ||| ||| |||||
TCGTGCCAGATGTATCAACGCTCTGCTGATATGGGACTTGGTGTTCCATTCAACATTGCATCATATTCTCTTCTGACATACATGATTGCTCATGTTTGCGgtatgttatcttctaccctgctatgtgactggataatcccaaaggtctaaccttattgatgtattgttcagcgtaagactgtttg-ttgttgatgttgtat------
upper sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 8
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaatatttagtctattgataacatgttgtggttttgtgggtgtaattggagata-atgtatcccatt----
|| || || |||||||| || ||||| |||||||| || || |||||||| || || ||||| ||| | |||||||||| ||||||||||| |||||||||| | | | | |||| | | | || || | ||| | | | | | | | |||| || ||||| |||
TCCTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTTTTGACATATATGATTGCTCAAGTTTGTGgtaggt---tcttatatgcatcactgtaatatttc--tactcagtgcaacgtttattgtgcaccttaatagaaaccttcttggttgtacatgtactgtatttgtg
upper sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G005990_T01 (Zea mays), 5'ss of exon 9
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaatatttagtctattgataacatgttgtggttttgtgggtgtaattggagataatgtatcccatt------
|| || || |||||||| || ||||| |||||||| || || |||||||| || || ||||| ||| | || |||||| |||||||||||| |||||||||| | | || || || || || || |||||| | || | | | | | ||||| || ||||| || |
TCTTGCCAGATGTATCAACGCTCTGCAGACATGGGGCTTGGTGTTCCATTCAACATCGCATCATATTCTCTCCTGACATACATGATTGCTCAAGTTTGTGgtagg-----ttttaaatgccttactctaatatttccc-cttagtccaatgtttattgtgcaccttaatacaaaccttattggttgtactgtatatcagtattcta
upper sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 5'ss of exon 10
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaata-tttagtctat-tgataacatgttgtggt-tttgtgggtgtaattgga--gata-atgtatcccatt
||||| |||||||| |||||||||||||||||||| || || || || ||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||| || ||| || | || ||| | ||| || | || || || | ||| | || | || | || ||||| | ||
TCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAACATGCATGATCGCTCATGTTTGTGgtatgca--tttgtgacaaatccag---aaacctaaccagttttgttcacatgcaaatttgctagaacgtttaaatatctagatagatgggtacatgtaggc-atc
upper sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 5'ss of exon 8
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaa--------attattgaagcatttgctttagacttaaat--atttagtc-tattgataacatgttgtggttttgtgggtgtaattgga--gataatgtatcccatt--------------------------------------------------
|| ||||||||||||||||| |||||||| ||||| || || || |||||||| ||||| |||||||| | ||||||||||||||||||||||||||||||||| | | ||| | | | || || ||| || |||| || | ||| | ||| | ||| | | | | | | ||
TCCTGTCAAATGTATCAGCGCTCTGCTGATATGGGTCTTGGTGTGCCATTTAACATTGCTTCTTATGCTTTATTGACATGCATGATTGCTCATGTTTGTGgtatgtatttatttctactatgagaatgtaaacctttgaaataagaggatctagttataatttctccatagttctatttcatttctgtcctggcattggcatcatgagttatcaatcatctacacccttttaaaaatccctctacattaatttgcctgtacagMapped 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|20498259|gb|BQ273189.1|BQ273189EST: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTG ATCTCATTCCAGGTGATTTTATCCATGTTATTGGGGATGCACATGTTTACT
genomic: TAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaat ... ttcttgtcagATCTCATTCCAGGTGATTTTATCCATGTTATTGGGGATGCACATGTTTACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGACATGCATGATTGCTCATGTTTGTGgtatgcaaattattgaagcatttgctttagacttaaatatttagtctattgataacatgttgtggttttgtgggtgtaattggagataatgtatcccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggtg