Sequence
atgc intronic sequence ATGC exonic sequencegtatgttccaaatgtgctctgaaattcaaagtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataacatggaagctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G38740.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g60440.1 (Oryza sativa), 3'ss of exon 14
----gtatgttccaaatgtgctctgaaattcaaagtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataacatggaagctattttg-cagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
| | |||| | | || ||| | | || | | || ||| | || | || | || || || | ||||||||| ||||| || ||||| || ||||| || |||||||| |||||||||||||||||||| || || |||||| ||| ||| |
cctggagttctccattcccttgcctagatatcgagttcatttt-ctgtttgtactaa-ataagtaaatagtcattcct---aacaatgtttg-gctattttgacagACTAGGAAAAGGGTATTGATCAACGCATTTACTGTCCGTGCATTACGTGATACCTTCCCCCCTGCTCGAGCAGCTG
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 14
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 14
gtatgttccaaatgtgctctgaaattcaaagtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataacatggaa--gctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
|| | |||| | || | | | || ||||||| |||| ||||||| | || | | | ||| || | ||| | |||||||| || ||||| |||| |||||||| ||||| ||||||||||||||||| || || || || |||| ||| |
--atatgaaaaata-gaactatgtatagcctggagatggattttatttgctaattctagcatagtgtttgcttctttgctgacaaggctttgttatctgacagACAAGGAAGAGAGTACTGATCAATGCATTCACAGTTCGTGCATTACGTGATACCTTCCCTCCGGCCAGAGCAGCTG
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 14
----gtatgttccaaatgtgctctgaaattcaa----agtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataacatggaagctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
|| | | || | || | | || | ||| | | | || || | ||| || | | || | |||| | ||| |||||||||| |||||||||||||||||||| |||||||| |||||||| |||||||| |||||||||||| |||| ||||
gttagtctctagcagctttgtttttttcttttcttttgattccttgttacctttgtggatatattcttttgtttgtccctaatcaataatcatg-attatatgatgcagACAAGGAAAAGAGTTTTGATTAATGCTTTTACAGTGCGTGCATTGCGTGATACATTTCCACCTGCTCGAGGTGCAG
upper sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 14
gtatgttccaaatgtgctctgaaattcaaagtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataaca----------tggaagctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
| | | || || || | ||| | | || |||||| || || | | | ||||| || | | | ||| ||||||| || |||||||||||||| |||||||||||||| |||||||| ||||||||||| | ||||| |||||||||
---------aggtagtgtttgtcatctaatgataactgga--taagttcataatgatatgatgtgtcctcaagtggaaatgtcaactgacggggttggatctacaatgcagACTAGGAAAAGAGTTTTGATAAATGCATTTACAGTTCGTGCATTGCGTGATACTTTCTCTCCTGCCCGAGGAGCAGMapped 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|17021829|gb|BM092863.1|BM092863EST: CAAATACTACCATATTATTAGGCAATATTGGAAGTTACTTAAACGAAGGA ACAAGAAAAAGAGTTTTGATTAATGCATTTACAG
genomic: CAAATACTACCATATTATTAGGCAATATTGGAAGTTACTTAAATGAAGGAgtatgttcca ... tattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAG
EST:
gi|12490066|gb|BG043587.1|BG043587EST: CAAATACTACCATATTATTAGGCAATATTGGAAGTTACTTAAATGAAGGA ACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGAT
genomic: CAAATACTACCATATTATTAGGCAATATTGGAAGTTACTTAAATGAAGGAgtatgttcca ... tattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaataatgttagcatatttttctttggtgaaataacatggaagctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
aaataac putative branch site (score: 2)
ctatttt putative PPT
atatttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttccaaatgtgctctgaaattcaaagtgtgctgtgctttatttaataatgttagcatatttttctttggtgaaataacatggaagctattttgcagACAAGAAAAAGAGTTTTGATTAATGCATTTACAGTCCGTGCATTACGTGATACTTTTCCACCTGCTAGAGGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG