Sequence
atgc intronic sequence ATGC exonic sequence...tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA17G20610.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 5
---tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgt--gatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
| | |||| | | | || | ||| | | | | || || | | | ||| | | | | || | || || | | ||||| ||||| || || ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| ||||| || |||| || ||||| |||
actttctgtagtag--tgaaaagaagagagaactttcgctag--atttttctcgatgtgattgctgcctggataatattgtactgttgctttctgattt-tgcagTCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
tacaata-gtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatc-tgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| | | | |||||| || | | || | | | || | | | | | | | ||||| | | || | | ||| ||||||||||| || |||||||||||||| || ||||| ||||| ||||| |||||||| || ||||| || |||| |||| || |||||||||
taaatttcatttgcttacaa-tacactatactggcattactttaggacattatctggtttactctaataagcaaatgataaaagacaatctt-tttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttcccca--aatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| || | || | ||| || || | |||| | ||| | ||||| |||| | | ||| || || | | | ||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| || ||||| |||| ||||||||||||
-ggcttaatgtttacacgatagtagtagaatgatgaata-tgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 6
tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttcccca--aatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| || | || | ||| || | || | | | ||| | |||||| |||| | | ||| || || | | | ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || ||||| ||| ||||| |||| ||||||||||||
-ggcttaatgtttacacgatggtagtagaataatgaatatgatcatagc-gttgtcagttttcttttaactaacaataccatgcatttttcattctctgcagTCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
----------tacaatagtggatttacaactatagatgat-cattgtt--tcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
| | || ||| | | | | || || | | | | || | | || | | | |||| | || || | | ||| |||||||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||| ||| |||| || || ||||||||||||
gtatcacaaatgattttgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
---tacaatagtggatttacaactatagatgatcattgtttcctgt-tgtttttgttttgagtttttttttccccaaatctgattgatg-gtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| | | | | | ||| | || | | | ||| |||||| | ||||| ||| | | ||| | | | ||| || | ||| |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | || ||| || ||||||||||||
tcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttga-----tttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------------------------tacaatagtggatttacaactatagatgatcattgtttcctgt-tgtttttgttttgagtttttttttccccaaatctgattgatg-gtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| | | | | | ||| | || | | | ||| |||||| | ||||| ||| | | ||| | | | ||| || | ||| |||||||| || |||||||| ||||||||||||||||| || ||||||||||| ||||| ||||| | | || ||| || ||||||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctttacctacatgtgtttcctactaagtgtctgttttcgctttga-----tttctgctcaagtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 5
tacaatagtggatttacaacta-tagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
|| || || || | | | | ||| | |||| || | | | | || || ||| ||| | || | |||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| ||| ||||| || |||||||||
agcatctgtacatcagcattcaatgggtattcaatcccctttgttcacgttatcctaggatcattattatttgctcaaatctgacagtggcactt-ctcagTCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAGMapped 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|17152867|gb|BM142800.1|BM142800EST: ATGGAAGCCCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG TCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATAT
genomic: ATGGAAGCCCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAGgtaaggtttt ... atttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
gattgat putative branch site (score: 4)
tttgccc putative PPT
ttttgagttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttccccaaatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT