Sequence
atgc intronic sequence ATGC exonic sequence...ttctctttgatctatttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
Basic information
species | Glycine max |
transcript | GLYMA13G17170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g26800.1 (Oryza sativa), 3'ss of exon 1
ttctctttga-tcta--tttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
| | | | |||| ||| | | | | | || | | | | | | | || || || | | |||| ||| | | ||||||||| ||||||||| |||||| |||| || || ||||||||||| || || ||||| |||||| | ||||| || | || ||||||||| | |
tgcaatgcgggtctagttttttcttacttaaaattttctgttactttttacagtttggtgcatttct--taccaactgagtcaacttttact-tatatgtaagGATGAAAGATATTGGCCGTTGATGTCTCCGTTACCATCATATGGGTACGGAAGAGAGCACAGGGGGCCTAGGTATGGGAGCCTTATACATGGTCAAGACC
upper sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G348602_T01 (Zea mays), 3'ss of exon 1
ttctctttgatctatttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
| || |||| |||| || |||| || || || ||||||||| || || |||||||||||||| |||| || ||||||||||||||| |||||| || || |||| ||| || | |||||||| || ||
----------------------------------------------gtgagct--tatttaactggca------ttgtgatgttttctgg------acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G047414_T01 (Zea mays), 3'ss of exon 1
ttctctttgatctatttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggct----aacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
|||| | || || | | | ||| || | | || | | | | || | ||||| | |||||| | ||||||||| || || |||||||||||||| |||| || ||||||||||||||| |||||| || || |||| ||| || | |||||||| || ||
cagagtttggtagatgcctatggt-gcttat---ttgggggcacaaatgcccacatttcagattgtgagcttatttaactggcattgtgatgttttctggacagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
------ttctctttgatctatttctttcat-tacat-------atctcttccactctctcat----aagtaaacattttactgac------actatatttgtcatcttacgt--gatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
|| || |||| | | | || || | |||| || | | || | | |||| | || | || ||| | | | || | | | |||||||||| |||||| | ||| | ||||| || ||||||||||| ||||| || ||||||| ||| ||||| ||||| ||||| |||||||| || |||
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
upper sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 1
--ttctctttgatctatttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
| || | | |||| | | || || | | | | || ||||| || ||| || | | | | || ||||| |||| ||||||||||| || ||||||||| |||||||||| ||||||||||||||||||||||| ||||||| ||| |||||||||| |||||||||||||||||| |||
gatattcaataaactatca-tattatgactagtgttagcatttatcgtataagcgaa-gtttggcttattttggttctttcttcttatgtgacatttaacagGATGAGAAGTATTGGCCACTGATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATCMapped 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|7589017|gb|AW704800.1|AW704800EST: CCTAGCTGAAGATGCTGTTATACTTGGCATTGAT GATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGG
genomic: CCTAGCTGAAGATGCTGTTATACTTGGCATTGATgtcagttttc ... tggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGG
EST:
gi|213595647|gb|DB962461.1|DB962461EST: GCCACATGACTCTCTTCCTAGCTGAAGATGCTGTTATACTTGGCATTGAT GATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGT
genomic: GCCACATGACTCTCTTCCTAGCTGAAGATGCTGTTATACTTGGCATTGATgtcagttttc ... tggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
taaacatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctttgatctatttctttcattacatatctcttccactctctcataagtaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatc