Sequence
atgc intronic sequence ATGC exonic sequence...tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
Basic information
species | Glycine max |
transcript | GLYMA06G46270.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g32800.1 (Oryza sativa), 3'ss of exon 4
tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
|| |||| | | | | || || | || | | | || | | | | | | | |||||| ||||||||| || |||||||||||| | ||||||||||||||||| |||||||| |||||||| || ||||| || || || ||||||||||| | ||||| |||
gacttagaatacccaggcatctgctattaattgaattgaaatcctgaaatattaaccttctcttggatacacacatctttgttttttttttctgatgtagGTACCTTGTCCCTGCTGATCTTACTGTTGGCCAGTTTGTCTATGTGGTTCGGAAGAGGATTAAGCTTAGCCCAGAAAAGGCCATCTTTGTCTTTGTGAAG
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0059g00660.t01 (Vitis vinifera), 3'ss of exon 4
-tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttgga---tgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
||||||| | | | | | | || | | | || ||| | | | || || || | ||| | | | || ||||| || || || || ||||| ||||| ||| ||||||||||||||||||| ||||| || |||||||| || ||||| | ||| |||||||| || ||||||||| | |||
agtatttgaaggctta--tagccagcttctat-tcatgtaatgggggttccatattttctaattctgctatgtgctttatcttttctttggggtttggat-cagATACCTGGTTCCTGCGGATCTGACTGTTGGCCAGTTTGTTTATGTTGTCCGGAAGAGGATTAAGCTCACTCCTGAGAAGGCGATATTCATTTTTATCAAG
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 3
---tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
| | | | | | | || | || | || | | || | | | | || || | || | || ||||| ||||| ||| | || |||| || || || |||||||| || | || ||| | || |||||||| ||||||||||||||||||||||| || |||
gccgtgcctctaggactgccagcctgcgtgtggtaacgtgcc--ctgtgtgtcgtcagcctaaccccgtaaacctcttggcgtggcctcccggccgc-tgcagGTACCTGGTGCCTTCAGACCTGACCGTCGGGCAATTTGTGTACGTCATCCGCAAGCGGATAAAGCTGAGCCCCGAGAAGGCCATCTTCATTTTCGTGAAG
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S209_115V6.2 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------tcatttgaatgttcga-gtgaatacatgcc--atc-ttgtttcatctcttttcttt-----cctctttatttatggtgtgtattattgttcttttttggatgaatgt----agGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
| || | || |||| || || || | | ||| || | | | | | | || ||| | || | |||| ||| ||||||||||| || || || ||||| ||||| ||||||||||| ||| | ||||| | |||||| ||||| | ||||||||||||||||| || || |||
gtgggtccccgtcgctttttgcgtttcgagattgagaggctgttggtggtgtcgtcgagtattaggtttgggatgcgttgtgatcacgtgtttggtcactaatccatgtccctgcaacagaagcatggctgtgtagagtgcggatacggagagtaacgtggaaaggtgtgcgcagGTATCTGGTACCAGCGGACTTGACGGTTGGACAGTTTGTGTACGTGATAAGGAAGCGCATCAAGTTGAGTTCGGAGAAGGCCATCTTCATATTCGTGAAG
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 3
--------------------------------------------------tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
|| | | | || | | | | | ||| || | ||| | || ||| | | || | | || | || | ||||| || ||||| |||||||| || ||||||||||| || |||||| | |||||||| ||||| ||| ||| |||||||| |||||| |||| || |||
gtaagcgctctctctctctctctctctctctctctctctctctctctctctctctcggactccggaattactcta---aagcttacgcaattctctctctcttctgggaattactctaaagctttcgcgcgatcttct---tgctcgcagGTACCTCGTCCCGGCTGATTTAACCGTTGGCCAGTTCGTCTATGTGATCCGGAAGAGGATCAAAGTGACTCCGGAGAAGGCAATCTTCGTTTTCGTCAAG
upper sequence: GLYMA06G46270.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 3
--------------------tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
|| | | || | | ||| | |||| || | ||| | || ||| | | || | | || | || | ||||| || ||||| |||||||| || ||||||||||| || |||||| | |||||||| ||||| ||| ||| |||||||| |||||| |||| || |||
gtaagctctctctctctctctctctcagagactccgg-aattactctaaagcttgcgcaattctctctctcttctgggaattactctaaagctttcgcgcgatcttct---tgctcgcagGTACCTCGTCCCGGCTGATTTAACCGTTGGCCAGTTCGTCTATGTGATCCGGAAGAGGATCAAAGTGACTCCGGAGAAGGCAATCTTCGTTTTCGTCAAGMapped 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|5677536|gb|AI938666.1|AI938666EST: ATTGTTGAAAGGGCAGAGAAGAGTGATGTTCCTGAAATTGATAAGAAAAA GTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCG
genomic: ATTGTTGAAAGGGCAGAGAAGAGTGATGTTCCTGAAATTGATAAGAAAAAgttagtttct ... atgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
tattattgttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttgaatgttcgagtgaatacatgccatcttgtttcatctcttttctttcctctttatttatggtgtgtattattgttcttttttggatgaatgtagGTATCTGGTCCCTGCTGATTTGACTGTTGGCCAGTTTGTGTATGTGGTGCGGAAGAGAATCAAGCTGAGTCCCGAGAAGGCCATCTTCATTTTTGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - -tgaatgt
- - - - - - - - - - - -catgcca