Sequence
atgc intronic sequence ATGC exonic sequence...ctcgaactctatctattttgctttacatgtctctttccctcactcttgattaaaacattttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
Basic information
species | Glycine max |
transcript | GLYMA09G08270.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G348602_T01 (Zea mays), 3'ss of exon 1
ctcgaactctatctattttgctttacatgtctctttccctcactcttgattaaaacattttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
| |||| || | || | ||| | || ||||||||| ||||| |||||||||||||| ||||| || |||||||||||||| |||||| || || |||| | | || | |||||||| || |||
---------------------------------------------------------gtgagcttatttaactggcattgtgatgttttctgg---acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G047414_T01 (Zea mays), 3'ss of exon 1
-----ctcgaactctatctattttgctttacatgtctctttccctcactcttgattaaaacattttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
| | | |||| ||||| | | | | | || | | | |||| || | || | ||| | || ||||||||| ||||| |||||||||||||| ||||| || |||||||||||||| |||||| || || |||| | | || | |||||||| || |||
cagagtttggtagatgcctatggtgcttatttgggggca--caaatgcccacatttcagattgtgagcttatttaactggcattgtgatgttttctgg---acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------ctcgaactctatctattttgc-tttacatgtctctttccctcactcttgattaaaacattt--tacttactttatgtttg-ttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
| | ||||| | ||| | | | | ||| || || ||| || || | | || | || | || | ||| | || ||||||||||||||||| | ||| | || | || ||||||||||| |||||||| ||||||| ||| ||||| ||| | ||||| |||||||| || ||||
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 1
ctcgaactctatctattttgctttacatgtctctttccctcactcttgattaaaaca---ttttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
|| | | | | | | ||| || | || | | | || | ||| |||| ||| | | | || | ||||| |||||||||||| |||||||||||| ||||||| | |||||||||||||||||||| || ||||||| ||| |||||||| | ||||| ||||||||||||||||
---gatattcaataaactatcatattatgactagtgttagcatttatcgtataagcgaagtttggcttattttggttctttcttcttatgtgacatttaacagGATGAGAAGTATTGGCCACTGATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATCMapped 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|209721330|gb|BW665796.1|BW665796EST: GTCATATGACGCTCTTTCTTGCCAGAGATTCTGTCATACTTGCAGTTCAG GATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGA
genomic: GTCATATGACGCTCTTTCTTGCCAGAGATTCTGTCATACTTGCAGTTCAGgtgctttttc ... tgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattaaaacattttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
tacttac putative branch site (score: 1)
taaaacattttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcgaactctatctattttgctttacatgtctctttccctcactcttgattaaaacattttacttactttatgtttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtgt