Sequence
atgc intronic sequence ATGC exonic sequence...tcatcatttattttaagtgtacataatcattgtttctcccattctttgatcgaatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA03G00670.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 8
tcatcatttattttaagtgtacataatcattgtttctcccattctttgatcgaatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
|| | | ||| || | | | ||| | || | | | | | | | | || || | || |||||| ||||||||||| |||||||| | |||||||||||| |||| ||||| || ||| |||||| || |||||||||| || ||| |||||
----------------gta-agacaatttatgatccccgcataaat--atggtagcttgatttccctcccaccctgaaaattcta----atgt-ttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 8
----tcatcatttattttaagtgtacataatcattgt--ttctcccattctttgatcg-----aatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
| |||| | || || | ||| ||| || | ||| | | | ||| | || | ||| | | | || | | | || |||||| || ||||| |||||||||||||| |||||||| |||||||||| ||||| || ||||| |||||||| ||||| ||||| |||||
gtaagttgctcttatgatttgtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccagATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------------------------tcatcatttattttaagtgtacataatcattgt---ttctcccattctttgatcg-aatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
| |||| | || | | | |||| || || || | || | | || || | | | | | | | | | | ||||||||||||||| || |||||||||||||||||||| || | || |||||||| |||||||||| | || || || ||||| | |||
gtaagtttctgaattttactgatagatgtaattcaaacagcaattgaaagtagtagacttatcgatgtgtcgagatggtttcctttttaccatgagcat-tgcactttttgtaaattttcaagggctactgcagcaactccggggttccttgtttgtgtttcttatttctttaattgctacagATACAAGAATGATCCAGAAATTTTGGCAATGACAAATTTAGTGGCTGCCTATCAAAGGAATGAAATTCTTGAGTTCGAAAAAATTCTCAAG
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 8
-tcatca-tttattttaagtgtacataatcattgtttctcccattctttgatcgaatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
| ||| |||| | | |||| || | || | || | | | | ||||||| | |||| | | | | ||| |||||||||||||| |||||| |||| |||||||| ||| | || || ||||| |||||||||| | |||||||||||||| | |||
gttgtcactttaccaaatatcggtataacgatcaa--caaatatgatgacatgttactgtattttgccatctgtttctgatgcggtatctgtcttgctacagGTACAAGAATGACCCAGAAATTCTGGCTATGACAAATTTGGTGGCTGCTTATCAAAGGAATGAAATCCTTGAATTTGAGAAAATTCTCAAGMapped 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|58014800|gb|CX701542.1|CX701542EST: ATGTTGATGGAGTCTGAAGTAAATCCTTTTGATGGGCAGGAGGCTAAGCC ATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTA
genomic: ATGTTGATGGAGTCTGAAGTAAATCCTTTTGATGGGCAGGAGGCTAAGCCgtaagtcctc ... cgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcgaatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
ctttgat putative branch site (score: 5)
ttgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatcatttattttaagtgtacataatcattgtttctcccattctttgatcgaatttcctccctctttctgttttcaccgttgtatatcacgtattgcagATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - -agtgtac
- - - - - - - - - - - - - - - - -ttctccc