Sequence
atgc intronic sequence ATGC exonic sequenceCTTCGTTTTCCAGTGGAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctccttcttcttcatctattttcaatttccaaacactcaccaattcgcttcttgtcttctgattctcgagattttttttctgtttacgt...
Basic information
species | Glycine max |
transcript | GLYMA04G42900.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os04g59550.1 (Oryza sativa), 5'ss of exon 2
CTTCGTTTTCCAGTGGAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctccttcttcttcatctattttcaat--ttccaaacactcaccaattc--gcttcttgtcttctgattctcgagattttttttctgtttacgt
| || | | || | | | || || ||||||| |||||||||| |||||| ||||| ||||||||| |||||||||||||||| ||||| | | ||| ||| | | | | | |||| | ||| || |||| | ||| ||| | | | | | | |
CACCGGCGGTGGGCTGGGCAACCTGCGCGCGCTGCTGGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagatttcctctctctccctggatccctccccttccttcctttctctctccgattcaagattccattctcccctcttcaatggatatcctgccaaac----
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G127591_T03 (Zea mays), 5'ss of exon 1
CTTCGTTTTCCAGTG-GAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgtt--cctgc--tatctcctt-cttcttcatctattttcaatt-----tccaaacactcaccaattcgctt-cttgtcttctgatt-----ctcgagattttttttctgtttacgt---------------------
|| || | | || | | | | | ||||||| |||||||||| |||||| ||||| ||||||||| | |||||||||||||| |||||| || || ||| | || |||| |||| || ||| || | ||| | | | | || || || || || | | | || | |||
-GGCGCCGGCCGGCCTGGGCACCCTGCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATGAACAAGTGGATCTTCCAGgtttacccgcattatattctagcttccccatccatcttccgccgcggatctggatgtcagatgcttctcctgcccggctgctacttttctcctttggaatatctaactaaattcgtccatactgcttaccattatag
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G127591_T01 (Zea mays), 5'ss of exon 1
CTTCGTTTTCCAGTG-GAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgtt--cctgc--tatctcctt-cttcttcatctattttcaatttccaaacactcaccaattcgcttcttgtcttctgattctcgagattttttttctgtttacgt
|| || | | || | | | | | ||||||| |||||||||| |||||| ||||| ||||||||| | |||||||||||||| |||||| || || ||| | || |||| |||| || ||| | | | | |||||| | | | | || | |||| | || || |
-GGCGCCGGCCGGCCTGGGCACCCTGCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGCTTCAACGTCACCGTCATCATCATGAACAAGTGGATCTTCCAGgtttacccgcattatattctagcttccccatccatcttccgccgcggatctggatgtcagatgcttctcctgcccggctgct----acttttctcct-ttggaat
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G040033_T01 (Zea mays), 5'ss of exon 1
CTTCGTTTTCCAGTGGAGC-GTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctc-cttcttcttcatctattttcaatttccaaacact-caccaattcgcttcttgtcttctgattctcgagattttttttctgtttacgt--
| | | || || ||| | | | | ||||||| |||||||||| ||||| ||||| ||||||||| |||||||||||||||| ||||| || | || | ||| |||| | | | | | | | |||||| || || ||| | | | | || | | || |
-CAAGATGGGGAACGGCGCCACCATCCGCGCGGTGCTCGCCATCCTCCAGTGGTGGGGATTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtcccgtccctcgcgcttgctcttgtttaaatcctggtcttctttttttgtttcaattcaatt----tccagagatggccatgtatgtagttatatatatattc
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: AT1G77610.1 (Arabidopsis thaliana), 5'ss of exon 1
CTTCGTTTTCCAGTGGAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctccttc--ttcttcatctattttcaatttc--caaacactcaccaattcgcttcttgtcttctgattctcgagattttttttctgtttacgt-------------------------------------------------
|| | | | || | |||||||||| || | || ||||||||||||| |||||||| || ||||||||| | ||||| ||||||||||||||| || || ||| || || | | | |||| || || | || ||| | |||||| | ||||| | || || |
AATCATGGAGGAAGGAAGTATGTTCAGATCTCTATTAGCGATTCTTCAGTGGTGGGGTTTCAATGTTACCGTCATCATCATGAACAAATGGATCTTTCAGgtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcag
upper sequence: GLYMA04G42900.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 5'ss of exon 1
CTTCGTTTTCCAGTGGAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctccttcttcttcatctattttcaatttccaaacactcaccaattcgcttcttgtcttctgattct-cgagattttttttctgtttacgt
| ||| ||||||||||| | |||||||| | |||||||||| ||||||| ||||||||||| || || ||| | ||||||||||||||||||||| | | ||| ||| || | | | | | | | | | || | | ||| | ||| | |||||| | |
TCTTCTTTGCCAGTGGAGCGCGTTTAGATCTCTGCTTGCCATCCTTCAATGGTGGGGGTTCAATGTCACCGTGATTATCATGAACAAGTGGATCTTTCAGgtttgctttctgcttttcagattctcaaatcccccctctttcggcttttgtcgaatggatttcatttccttaattttgttttattctgtttctggatgtg-Mapped 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|192296166|gb|FG989751.1|FG989751EST: GGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAG AAATTGGATTTCAAGTTTCCCTTATCAGTTTCCTGTGTCCACTTTATCTGT
genomic: GGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgcta ... gttgttacagAAATTGGATTTCAAGTTTCCCTTATCAGTTTCCTGTGTCCACTTTATCTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTCGTTTTCCAGTGGAGCGTTATCAGATCTCTCTTGTCCATCCTTCAGTGGTGGGCCTTCAATGTCACTGTCATCATCGTCAACAAGTGGATCTTTCAGgttcctgctatctccttcttcttcatctattttcaatttccaaacactcaccaattcgcttcttgtcttctgattctcgagattttttttctgtttacgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA