Sequence
atgc intronic sequence ATGC exonic sequence...tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
Basic information
species | Glycine max |
transcript | GLYMA02G29160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
tggagaacaacacctaaaacagaatggaact-gtatctaagttgtcctttggtttttgatgatttt---tctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
| | | || || |||| | | | | | | |||| ||| || || | ||| |||||| | | || ||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||| | || || |||||||| ||||||||||| ||||| || || || |
---gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaattt-cagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
tggagaacaacacctaaaacagaa-tggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
||| | ||| | | | || | | || || | | | | | | | ||| | | ||||||||| |||||||| |||||||| || | ||||||||||| ||| ||||| || || |||||||| ||||||||||| || ||||| || |||
-tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcagcgcgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S381_21V6.1 (Physcomitrella patens), 3'ss of exon 2
tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttg----tgttcaattt--tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
| | || | | | || | | | |||||| | || | | || | | ||||| || | || | ||||||| || || || ||||| |||||||| | |||||||| || ||||| || || || ||| | ||||||||||||||||| || ||||| || |||||||
-----ctgcattcttagatttgtagtttgctaccttaatgcagtccttcg-cgttaggcgtcagttgttgtggaagattgatccaaaaatggtgcatgtaatgcagGCCGGTTTCGCGGGAGACGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
tggagaacaacacctaaaacagaatggaactgtatc--taagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtgttcaatttt---gcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
||| | || | | | | |||| | | || | | || | | || | | || | | || | ||| ||||||||| || ||||||||||| || || | || ||||| || ||||| ||||| || || | ||||||||||||||||| || ||||| || |||||||
-----aaccttaacttgcgtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
tggagaacaacacctaaaacagaatggaactgtatct---aagttgtcctttggtttttgatgatttttctctttcggtgttgat-ttgtgttcaattt-tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
|| | || | | | || | | | || | | | | | | | ||||| | ||||| | ||| |||||||||| || ||||||||||| || || | || ||||| || ||||| ||||| || || | ||||||||||||||||| || ||||| || |||||||
-----gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S381_18V6.2 (Physcomitrella patens), 3'ss of exon 2
-tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttt--tgatgatttttctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
| | || | | ||| | | |||| |||| || | | | | | | | | | | | | || || | ||||||| || || || |||||||||||||| | |||||||| || ||||| || || || ||| | ||||||||||||||||| || ||||| || |||||||
gtagtatcaaatctccacaaccgtct---tctgtgtctaggtcatgttggacctgtgtttaggccaatcaacatgtaggagtaatatggtgcatgtaatgcagGCCGGTTTCGCGGGAGATGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtg---ttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
| | | || | ||||| | | | | ||||| | | | | ||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||| || || ||||| || || ||||||||||||||||| ||||| |
----------------------------------------------gtgcgctcctggcgcggtttct-tgtggattttgatccggggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG
upper sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtg---ttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
| | | || | ||||| | | | | ||||| | | | ||||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||| || || ||||| || || ||||||||||||||||| ||||| |
----------------------------------------------gtgcgctcctggcgcgatttct-tgtggattttgatccggggggtgtgtttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATGMapped 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|254324687|gb|GR834112.1|GR834112EST: GTGAGGATATACAACCTCTTGTTTGTGATAATGGAACTGGAATGGTCAAG GCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTG
genomic: GTGAGGATATACAACCTCTTGTTTGTGATAATGGAACTGGAATGGTCAAGgtatgtatat ... aattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTG
EST:
gi|209718162|gb|BW657808.1|BW657808EST: GTGAGGATATACAACCTCTTGTTTGTGATAATGGAACTGGAATGGTCAAG GCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTG
genomic: GTGAGGATATACAACCTCTTGTTTGTGATAATGGAACTGGAATGGTCAAGgtatgtatat ... aattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttggtttttgatgatttttctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
tgttgat putative branch site (score: 4)
tttttgatgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggagaacaacacctaaaacagaatggaactgtatctaagttgtcctttggtttttgatgatttttctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG
- - - -caacacc
- - - - - - - - aaacagaa
- - - - - - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttc