Sequence
atgc intronic sequence ATGC exonic sequence...ctgttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
Basic information
species | Glycine max |
transcript | GLYMA11G02520.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
ctgttgtttttgtctcaaggtgcgggttatct-atcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccat-agTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| | ||| || | | | ||| | || | || || | | ||| || | || |||| | || || || || | || ||||| | ||||| |||||||||||||||||||| || ||||| ||||| ||| ||||||||| |||||||| | || | | ||
-tatcctttgagtagtgtgccactgactattttattaggactg-atcatcctttgtttctcttcaaatttgatataatataattctctgtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
ctgttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtt-taacttctgatccat---agTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
| | | | || | || | | | | | | | || || | | |||| || | || | ||| || ||||| | ||||| |||||||| ||||||||||| |||||||| ||||||||| ||||||||| |||||||| |||| || ||||
-taatctaacggatcaggagtctcgcttgta---cgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
----ctgttg-tttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtt-tttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
|| | | | ||| | | || | | || |||| | | || ||| || || ||| ||| || | ||| | ||| | || |||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| ||||||||| |||||||| |||| || ||||
ataactctaaactatcatctgtcttgactagctaaatgtt-ttattgcacttggtcattatttgtttccttatttgaattg-ttca--ttatcatctatttca--gTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
-----ctg--ttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
||| ||||| | || ||| | | || | | || ||| | ||| || | | || ||| |||||| | ||| || | ||| ||||||||||| ||||||||||| ||||| ||||| ||||| | ||||||||| |||| |||||||| ||||| |||||| | || |||
ataaactgatttgttctcttcacaaaatattgaatagg-agaactcaaatgttata---tttcta-tgtcacccctgttttgatc--ggttatgttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 1
--ctg-ttgtttttgtct-caaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
|| ||| ||||||| | | |||| ||| | ||| | || | |||| || || ||| ||| ||| || | |||||||||||| ||||||||||||||||||||||| || | |||||||||||||| || |||| ||||||||| || || || ||||||
gattgcttgcatttgtctatttaatttaagcaatctgctatttct-catgcattattctttataattctgactttttttttttcttttg---cttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA
upper sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 4
------ctg-ttgtttttgtct-caaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
|| ||| ||||||| || | |||| ||| | ||| | || | |||| || |||||| || ||| ||| || | |||||||||||| ||||||||||||||||||||||| || | |||||||||||||| || |||| ||||||||| || || || ||||||
cagtgattgcttgcatttgtctatttagtttaagcaatctgctatttct-catgcattattcttta----tatatctgactttttttcttttg---cttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAAMapped 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|13478024|gb|BG507669.1|BG507669EST: CAACTGCTTGGAAGGGGGACATTTGGGCATGTATATCTTGGTTTTAACAG TGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGA
genomic: CAACTGCTTGGAAGGGGGACATTTGGGCATGTATATCTTGGTTTTAACAGgtattttgta ... tgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
ttctgat putative branch site (score: 3)
cttct CT-rich tract
atttgatttagtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgttgtttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtttttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ctgttgt
- - - - - - - - - ggtgcgg
- - - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg