Sequence
atgc intronic sequence ATGC exonic sequence...acaaagggtgattatggaacttgattttaattttatgttcagaaagcaagttttagataaccttaaatcttctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
Basic information
species | Glycine max |
transcript | GLYMA14G05400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G086418_T01 (Zea mays), 3'ss of exon 2
acaaagggtgattatggaacttgattttaattttatgttca-gaaagcaagttttagata-accttaaatctt--ctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
|| | || || | || ||||| ||| | | || |||| || | || | | ||| | ||| ||| ||| ||| ||| | | |||| || ||||||||||| ||||| || | |||||||||||| |||||||| | || |
---aaacatcatgttgctagttaattttgctttgttttccatgaaatgaaatctttctcacatcttgtagcttagttttggacttttgatactgaaataac-agGAACCATTTGTGAACATACCAGAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG
upper sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G086418_T02 (Zea mays), 3'ss of exon 2
------------------------------acaaagggtgattatggaacttgattttaattttatgttca-gaaagcaagttttagata-accttaaatctt--ctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
|||| | || || | || ||||| ||| | | || |||| || | || | | ||| | ||| ||| ||| ||| ||| | | |||| || ||||||||||| ||||| || | |||||||||||| |||||||| | || |
atatgatataattgaccactattccttctatcaaaacatcatgttgctagttaattttgctttgttttccatgaaatgaaatctttctcacatcttgtagCTTAGTTTTGGACTTTTGATACTGAAATAAC-AGGAACCATTTGTGAACATACCAGAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG
upper sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G086418_T03 (Zea mays), 3'ss of exon 2
acaaagggtgattatggaacttgattttaattttatgttcagaaagcaagttttagataacct-taaatcttctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
||| ||| || ||| |||| | ||| | | | | || | ||| ||| ||| ||| | | |||| || ||||||||||| ||||| || | |||||||||||| |||||||| | || |
-------------------tttgctttgttttccatgaaatgaaatc---tttctcacatcttgtagcttagttttggacttttgatactgaaataac-aggaaccatttgtgaacataccagAAGATAGAATCCGTGAAGCTCTAGAAGTCATCCTAG
upper sequence: GLYMA14G05400.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0059g01400.t01 (Vitis vinifera), 3'ss of exon 2
acaaagggtgattatggaacttgattttaattttatgttcagaaagca----agttttagataaccttaaatcttct---ttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
|| | ||||||||| | | || || || | ||| | || | || ||| | || | ||||| || ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||| ||||||||||||
-----ttgtacatgacatacttgatttcctataca-gtgaaggaaatattgtgatttgaaatgatatttaatgctacaaatttgatatctgaaattt-tgcattcagGAGCCTTTTGTGAACATCCCAGAGGATACAATCCGTGAAGCGCTAAAAGTTGTTCTTGMapped 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|12687931|gb|BG154327.1|BG154327EST: TCAAGTCAAATGGGATCAAGCTTTTTCAGTTTGGGATTGAGGGCCATAAG GAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTT
genomic: TCAAGTCAAATGGGATCAAGCTTTTTCAGTTTGGGATTGAGGGCCATAAGgtctatttct ... gtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaagttttagataaccttaaatcttctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
ctttaac putative branch site (score: 3)
ttaaatcttctttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaaagggtgattatggaacttgattttaattttatgttcagaaagcaagttttagataaccttaaatcttctttaaccttgtgaaacttgtgcatccagGAGCCTTTTGTGAACATCCCAGAGGACACAATCCGTGAAGCACTAGAAGTTGTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT