Sequence
atgc intronic sequence ATGC exonic sequence...agagaaatgcatatacactgattttatagttgcgtgtaaattaatcaatggctataaattgtaactcaattcatacatttttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT
Basic information
species | Glycine max |
transcript | GLYMA08G02060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
---agagaaatgcatatacactgattttatag-ttgcgtgtaaattaatcaatggctataaattgtaactcaattcatacatttttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT
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ttaacttctattaatctgcacc-attgagtacctttctcctttgttaaaatgctactataatctgggcattaattttaatgagttttttctcttc---caaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
upper sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------agagaaatgcatatacactgattttatagttgcgtg-taaattaatcaatggctataaattgtaactcaattcatacatt-tttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT
|||| || || | || | || ||||| ||| | ||| | |||| | || ||||||||||||| | || | | |||||||||||||||||||| |||| |||||||||||| |||||||| || ||||| |||| ||||||||||| || | |||||| || |||
gtatggttcttggtgcttttggagtgatgtttacttttggctgcagcattcttgtttccagttttccatgataaatcctacaaaatcagccaatc-tggctcagaactaccacaatttttttctttggtgtgacagCTTCTCGGTTCACCTGATGATGCAAGTCTTGGCTTTCTCCGAAGTAATAATGCCCGACGATATGTTAGGCAGCTTCCACAATATCCAAAGCAACAAATCTMapped 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|9898807|gb|BE607775.1|BE607775EST: CCTTGTTTCCTGGCAAAGACTATGTTCACCAACTAAGGCTTATAACGGAG TTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAAT
genomic: CCTTGTTTCCTGGCAAAGACTATGTTCACCAACTAAGGCTTATAACGGAGgtatggtttt ... ggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatggctataaattgtaactcaattcatacatttttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT
ttgtaac putative branch site (score: 2)
catttttttttctttg putative PPT
tataaattgtaactca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagaaatgcatatacactgattttatagttgcgtgtaaattaatcaatggctataaattgtaactcaattcatacatttttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -tgcatat
- - - - - - - - - - - - - - - tgcgtgt