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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggattaagaattattttagggattgaaaggcttcgtgtttattttagatattatatttggtgcttgtgttttataaatcaattcccttcattctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTGCTGGG

Basic information

species Glycine max
transcript GLYMA07G04040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G04040.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g41740.1 (Oryza sativa), 3'ss of exon 2
aggattaagaattattttagggattgaaaggcttcgtgtttat-----tttagatattatatttggtgcttgtgttttataaatcaattcccttcattcttt-cagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTGCTGGG
|| | | | || | | | | || |||| || |||||||| | | || | | | || | ||| | | | |||| || || || |||||| | ||||| ||||||| |||||| |||||||||||||| || || ||||| || ||||| ||||| || ||||| | ||||
--ctcctagtacacctatgctgacctgatatttgagcactcataagcgtttaactaatatatttg----tccagccatacataaccatgcgtttctctttctgcagAAAAGGAAAACTTGTGCCTTTATGGGTTTCCCAATGAGCATTGGGAAGTAAATTTGCCCGCAGAAGAGGTGCCACCTGAGCTCCCAGAGCCAGCATTGGG

upper sequence: GLYMA07G04040.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038066_T02 (Zea mays), 3'ss of exon 3
aggattaagaattatttta--gggattgaaaggcttcgtgtttattttagatattat--atttggtgcttgtgttttata-aatcaattcccttcattctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTGCTGGG
|| || | || | ||| | | ||||||| | || || | || | | || | || | | ||| | || | || |||| ||||| || |||||| ||||||| ||||| | |||| |||||||||||||| ||||||||||| || ||||| || || || || || | | ||
---atcccctgttttcataatgagatgtatactgatcgtgttattaataattaccacagatatatttctacagcttagcatgaccaagtgttctc--ttttgcagAAAAAGAAAACTTGTGCCTGTATGGGTTTCCTAATGAGAGCTGGGAAGTAAATTTGCCTGCTGAAGAGGTGCCACCTGACCTCCCAGAACCAGCATTAGG
















Mapped 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|192326234|gb|FK015826.1|FK015826
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|208308763|gb|GE104585.1|GE104585
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCC
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCC
EST: gi|192297449|gb|FG989513.1|FG989513
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|298192744|gb|HO033178.1|HO033178
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|192333136|gb|FK026465.1|FK026465
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|298172302|gb|HO019342.1|HO019342
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|151405473|gb|EV275287.1|EV275287
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGCATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|58014682|gb|CX701424.1|CX701424
EST:     CTGATGTTGAAGATTTTTCCAACCAATGTGATCCTG                         AGAAAGAGATTTTGTGCTGGTATGGCTTTCCCAGTGAGCAGTGGAAAGTAA
genomic: CTGATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|18039623|gb|BM307917.1|BM307917
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|208167333|gb|GD960841.1|GD960841
EST:     TTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: TTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
EST: gi|120532679|gb|EH260812.1|EH260812
EST:     ATGTTGAAGATTTTTACAACCAATGTGATCCTG                         AGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA
genomic: ATGTTGAAGATTTTTACAACCAATGTGATCCTGgttagttata ... attctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatattatatttggtgcttgtgttttataaatcaattcccttcattctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTGCTGGG
                                     ttcccttcattctttc  CT-rich tract
 tgttttataaatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggattaagaattattttagggattgaaaggcttcgtgtttattttagatattatatttggtgcttgtgttttataaatcaattcccttcattctttcagAGAAAGAGAATTTGTGCTTGTATGGCTTTCCCAGTGAGCAGTGGGAAGTAAATTTACCTGCTGAAGAAGTACCACCAGAGCTTCCTGAGCCCGTGCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - -gggattg
- - - - - - - - - - - - - - - -cttcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgct