Sequence
atgc intronic sequence ATGC exonic sequencegtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctttgacttccaagtgatttaacaaattcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
Basic information
species | Glycine max |
transcript | GLYMA03G31510.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g58330.1 (Oryza sativa), 3'ss of exon 6
---gtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctttgacttccaagtgatttaacaa------attcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
| ||| ||| | |||| || ||| | | | | | | | | || || ||| | | | | ||| |||| | || ||| | | |||| | |||||| |||||||| | ||||||||||||||||||||||| ||||| ||||||||| || | |
atcacaccttcactcaaggaatcaat-ttgagagtccttttccgtctctgctctttcatatcttttggttgttaaactgtatcttgctttattttcgttagGGGGAAGCAAGCGATAGTGGGGGCAACCAACAGATTTGGGAAAAGTGGTCAACGGATGGCACAGAAAGACAGGTAGCGAAGCTGATGGAAGAAGACATCG
upper sequence: GLYMA03G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g08440.1 (Oryza sativa), 3'ss of exon 5
----gtgattattgagaagaaatagttgttgaaagaattttattatttt------taatatctttgacttccaagtgatttaacaaattcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
|| || | | | | ||||| | || | | |||||| |||| | || | | || | ||| || ||| || | |||| ||| | | || | | |||||| |||||||| | |||||||||||||| |||||||| ||||| ||||||||| || | |
aatcatgttttgtcttgtgccacatttgtttgcatgcccttgtccgtcagtcacacaatatcgttgatctttaaactaaatcttgc-ttgaatggc-attagGGGGAGGCAAGTGACAGTGGGAGCAAACAACAGATTTGGGAAAAGTGGTCAACCGATGGCACAGAAAAGCAGGTAGCGAAGCTGATGGAAGAAGACATCG
upper sequence: GLYMA03G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G004356_T01 (Zea mays), 3'ss of exon 6
gtgattattgagaa--gaaatagttgttgaaagaattttattatttttaatatctttg-acttccaagtgatttaa--caaatt---cagtggt--gatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
|| ||| || |||| | || | || | | |||| | | | | || || || || | |||| | ||| |||| |||| ||| | | || | || |||||| |||||||| | || ||||||||||||||||| || ||||| ||||||||| || |||
--ccttgttgtgacttgaaaaaacaatttgactgtccttttccatcccgatatttccgtatctattggtcgttaaaattggatcttcctttggtttcgttagGGGGAAGCAAGTGATAGTGGGAGCAAACAGCAGATTTGGGAGAAGTGGTCAACGGACGGCACAGAAAGACAGGTCGCAAAGCTGATGGAAGAAGACATTG
upper sequence: GLYMA03G31510.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03040.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgattattgagaagaaatagtt-gttgaaagaattttattatttttaatatctttgacttccaagtgatttaacaaattcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG------------------
|| | | | ||| ||| || || ||| || | | ||| || || | | ||| || |||||| || || | | ||| | || | |||| | ||||| || ||||| |||||||| ||||| || || || |||||||| ||||||||||||||||
gttag-actagagagagatacttcattaaaaaaagaacagaactttggtaatggtttttcttgcactgactt----------gtggtgt-----aaaaactttcttcagG-ATGAGACGCAGGCC-GTGTGGGAGAAATGGTCAAACGATGGGACAGAGAGGCAAGTGGCTAAGCTGATGGAAGAAAACGTTGGAGCAGCGATGCAACTTTMapped 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|193431218|gb|FK398602.1|FK398602EST: CCGGTGCAGTGGCACCACTGGTAACTGACATCCCATTATCATCAGTCGAG GAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCATGGGACAAGTG
genomic: CCGGTGCAGTGGCACCACTGGTAACTGACATTCCATTATCATCAGTCGAGgtgattattg ... tggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatttttaatatctttgacttccaagtgatttaacaaattcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
atttaac putative branch site (score: 3)
ttttaatatctttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattattgagaagaaatagttgttgaaagaattttattatttttaatatctttgacttccaagtgatttaacaaattcagtggtgatcagGAAGAAGGTGGTGAAGGTGCGCGAAACCGGCCAGCTTGGGACAAGTGGTCGAACGATGGCACAGAAAGACAGGTAGCTAAGCTTATGGAAGAAAACGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA