Sequence
atgc intronic sequence ATGC exonic sequence...ctgattacacacacacactcacacatacagagagaccaattgacaacaaatcagaaaattatgacaaacaaccttatataagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
Basic information
species | Glycine max |
transcript | GLYMA06G13140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 5
ctgattacacacacacactcacacatacaga--gagaccaattg-acaacaaatcagaaaattatgacaaacaaccttatataagctctc--tttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
| | ||| | || | | | | || ||| | || | ||| || | | | ||| ||| | | | | |||||||| || |||||||||||||| ||||| ||||| || ||||| ||||||| ||||| || || || || || ||||| || | || ||||| || |
-----ctctctttttttttcatatatgccatttgttattatttatgcaaatatccatttatgtattccagatgatcccttattccctcatggtgtttttattcagAATGTCAAGACATTTAAAGATGTCAAAGGGTGTGATGACGCAAAGAAAGAACTCGAGGAGGTAGTTGAGTATCTAAAAAACCCTTCAAAGTTTACTCGGC
upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------------------------ctgattacacac-acacactcacacatacagagagaccaattgacaacaaatcagaaaat---tatgacaaacaaccttatat---aagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
|| || | | ||| | | | | |||||| || | || |||||| |||| || ||| | || || |||||||| || |||||||||||||| ||||||||||| ||||||||| | |||||||||||||| || || || || || || || | || || || ||||
gtatctgagtacgcttcataaagtacttggtgcaagaagagtatcttggtccattttgggttactacatgaactttattagtgttttccttctgcaccatactgtctttattgctgttgtttgacagtaatgtgatttctcagtacagaaaacaaatacatattcaaatgcttctatgctgtttcagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAAGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------------ctgattacacacacacactcacacatacagagagaccaattg-acaacaaatcagaa-aattatgacaaacaaccttatataagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
| || | |||| | ||| | | | | | || | | | | | | ||| | | || | ||| | | || |||||||| || |||||||||||||| ||||||||||| ||||||||| | ||||||||||| || || || || || || || || | || || || ||||
gtatctgattacgcttcataaaatacttgatacaagagtatcttggtccactttgggttactacaaaaacattattagtgtttttctttcgcaca-atactgtcttctggttgtctgttagtaatgtgatttctcggtacagaaaacaaatacatattcaaatgataattctatggttttacagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAGGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
-ctgattacacacacacactcacacatacagagagaccaattgacaacaaatcagaaaattatgacaaacaaccttata-taagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
| | || | | | | || ||| | || | | |||| || || ||| | | | | | || | | ||||||||| ||||||||||| || || || |||||||| |||||||||||||| || || || || || ||||| || ||||||||| | || ||||||||||
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtca--tttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
upper sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------------------ctgattacacacacacactcaca-catacagagagaccaattgac---aacaaatcagaaaattatga--caaacaaccttatataagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
||||| | | | ||| |||| || || || | || ||| |||| | | | || | | || | | ||||||||||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||||||||| ||||| ||||| ||||| || || || ||||| | |
gtagatatctgatgttacgtgttttgtattatatgttttaagagtgtttctggagatttcaagtctattgagcaagttgtgcaagtgatt-tagagttgtattcatttcatatggaccatcctgttttttgaagcatgccagttaattgtagtcctgttatttttctctgagtagttgcctttgctgcagAATGTTAAGACATTTAAGGATGTGAAAGGCTGTGATGATGCAAAACAGGAGCTTGAGGAAGTAGTGGAGTACCTCAAAAACCCTGCAAAGTTTACTAGACMapped 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|19348886|gb|BM893418.1|BM893418EST: GTAGTACATATGCTCCAAAGGAACTAAATAAAGAAGTGGTGCCAGAAAAG AATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAA
genomic: GTAGTACATATGCTCCAAAGGAACTAAATAAAGAAGTGGTGCCAGAAAAGgttaacattt ... cctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatcagaaaattatgacaaacaaccttatataagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
ctctctttcctcttgc CT-rich tract
aaaattatgacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgattacacacacacactcacacatacagagagaccaattgacaacaaatcagaaaattatgacaaacaaccttatataagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
- - - acacaca
- - - - - - - - - -cacacat
- - - - - - - - - - - - - - - - - - - - tgacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaacc