Sequence
atgc intronic sequence ATGC exonic sequence...agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA
Basic information
species | Glycine max |
transcript | GLYMA17G37870.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 19
----------------agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctctt---tctatgtattc-atgccaagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-
|||| || | |||| | | | | | | ||||| || | | ||| |||| | |||||| || | || || ||||| |||||||| ||| | ||||||||||| || |||||||| ||||||||||| || || || || ||| ||| || ||||| || || | |||||
gtaacaattactatgctgtttccttattga-attatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTG
upper sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctcttt----ctatgtattcatgccaagcctaa--catgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-
|| || | || || || | | ||| || || | ||| || | | | | | | ||| | || | | ||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||||||||| || || ||||| || |||| |||||| |||||||| || | |||||
---cttaatgtagcctctcgagaactg--ttattgca--tggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
upper sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM5G844195_T04 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------agttttctcaagaccattagacaaatggatggtggcaaatgtt--attaatct-ctttctatgtattcatgccaagcctaacatgatgat-------ctat--ctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-
|| | ||| | | | | || || |||| |||||| | || | | ||||| | || || ||| ||||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||| ||||| || || ||||| |||||| |||||| ||||||||||| | |||||
gtaatgattcttgttttatggctagttcatttccccctcaatccccccttcaatccccatggggaatgggtgtatccaaagtagccttgtagcctcgcgagacctgttattgcatgaatcagctttctttaaatgaagtgctagcctctcttgtaaattacattgctactgctttctgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTATATGCGTGTTCACATCTTTTTTGGACTGATGACCAAGATGGTATAATGGATGGTG
upper sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 19
agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-
| | ||| | |||| | | || ||| | | |||| | | || | || || | || | | | | | ||||| ||||||| |||| | ||||| ||||| || |||||||| ||||| ||||||||||| ||||||||||| ||||||| |||||||||||||||||||
-------gtacaaatattttgccaatgatttct----cattttacaagctttcttctcaatttctatccaaacgcttatat-----tttctttgtgaccagTACTCAGCAAGGCTTCTTAAGAAGCCTGACCAATGCCGAGCGGTTTACGCATGCTCTCACCTCTTTTGGGTCGATGATCCAGATGGTATTAAAGATGGAG
upper sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 19
agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctctttctatgtattcatgcc-aagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-
| || | | | ||| | | | | || | || | | | | || || ||| | ||| || || |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||| || ||||| ||||||||||| ||||||||||| ||||| ||||||
----gtagtaatgtttacattctatctgattattttgact--tgttgaactttctatgccaaaagttgtttaaaccttttccttttgtctttccttggccagTATTCAGCAAAGCTTTTAAAGAAACCTGATCAATGCAGAGCAGTTTATGCATGTTCCCATCTTTTTTGGGTTGACGATCAAGATGGCATTAAGGATGGAGMapped 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|151411598|gb|EV281409.1|EV281409EST: AATGTCTTTGGCATTGAGAACAGGGATACATTAACACACAAGGCCACAGG GTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGC
genomic: AATGTCTTTGGCATTGAGAACAGGGATACATTAACACACAAGGCCACAGGggtatagtac ... tctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGC
EST:
gi|9564171|gb|BE473680.1|BE473680EST: AATGTCTNTGGCATTGAGAACAGGGATACATTAACACACAAGGCCACANG GTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGC
genomic: AATGTCTTTGGCATTGAGAACAGGGATACATTAACACACAAGGCCACAGGggtatagtac ... tctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatctctttctatgtattcatgccaagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA
gcctaac putative branch site (score: 2)
tctatctttcc putative PPT
tatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctctttctatgtattcatgccaagcctaacatgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat