Sequence
atgc intronic sequence ATGC exonic sequence...atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
Basic information
species | Glycine max |
transcript | GLYMA09G34950.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g16000.1 (Oryza sativa), 3'ss of exon 9
--atgatcttttttttcagacttttaagttataatctttattg-ccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
| | | | || | || |||||| | || ||| |||| | | || | | || | | || | || | | || |||| | |||||||| ||||||||||| ||||||||||| || ||||| ||||| || ||||| ||||| ||| ||||| || || || |||
gtgcaagcatataattgtcccctt---gttatatttttaattctccaagggtgaccaggggggaccagaatgctaactaagcattccttgtctgtcttcacagGTGGCTCCCAATGGGTGGTCTGAAGGGGAATGCAAAGGAAAAGCTGGCTGGTTCCCATCTGCCTATGTGGAGCAGAGGGACAAAGCCCCGGCAAGTAAGG
upper sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
| ||| | || || || | ||| || || | | | ||| | || | || | || || | || ||| | |||| | | || ||||| |||||||||| ||||||||| |||||||||||||| ||||| || ||||||| ||| || | || || |||||||
---gtatttcctgccacaccctt--tcaacaatacatacaa--aacagtgaaaaaaaatga--tttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
upper sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv02s0087g00190.t01 (Vitis vinifera), 3'ss of exon 9
atgatcttttttttcagactttta---agttataatctttattgccaatatcagactgatttgagctgtatttttattatcc---ttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
| | || || | ||| ||| | ||||| || |||| | | | | || ||||| | ||| || ||| | | || |||| | ||||| |||||||| || || |||||||| |||| || |||||||||||||||||||||||||| || | |||| || |||||| ||
----tttcttaatttatactcttatttacctataaaaaaagttaccaagttta--tcaaagttcattgaattttcaaaatctcatttctggccataatatcatcagGTGGCTCCCAACGGATGGTCGGAGGGTGAATGCAAGGGCACGGCCGGATGGTTTCCCTCTGCTTATGTAGAAAGGCGTGACAAAGCTCCGGCCAGCGTGA
upper sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ27680 (Selaginella moellendorffii), 3'ss of exon 8
atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
| ||| |||| | | | || | | || | ||| ||||| ||| ||| ||||| ||||||||||| |||||||| || ||||||||||| ||| | ||||| ||| | | | | || || |||||
------------------------------------------------gtgggtgac--gagccaaagtcattgaatgaatgaacgtttttcttttgcagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG
upper sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ37265 (Selaginella moellendorffii), 3'ss of exon 8
atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
| | | | | | | || || | | |||| ||| | |||||| ||| ||| ||||| ||||||||||| |||||||| || ||||||||||| ||| | ||||| ||| | | | | || || |||||
----------------------------------------gtgggtgacgagccaaagtca-ttgaatgaatga-acgtttttctttggcagGTTTCTA--------CCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAGMapped 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|7284902|gb|AW597389.1|AW597389EST: CTGAGGGGGAGTTAAGCCTATCAGTTGATGATTTTGTTGTAGTTCGTCAG GTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGG
genomic: CTGAGGGGGAGTTAAGCCTATCAGTTGATGATTTTGTTGTAGTTCGTCAGgtatttcctt ... acatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGG
EST:
gi|209713198|gb|BW681733.1|BW681733EST: GGGGGAGTTAAGCCTATCAGTTGATGATTTTGTTGTAGTTCGTCAG GTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGG
genomic: GGGGGAGTTAAGCCTATCAGTTGATGATTTTGTTGTAGTTCGTCAGgtatttcctt ... acatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
gactgat putative branch site (score: 3)
catttct putative PPT
tatttttattatcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtt