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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

Basic information

species Glycine max
transcript GLYMA08G20830.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
-------------------gttagatt-cccatgtttggatgagca--atgaatt-tctgctgctttatca-agttatagtaactggctcttttttttttggc----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                   | |  ||   ||||  ||   |||| |  |||||   |   ||  || |    ||| |   | | |      ||  ||  ||      ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||| ||| || ||||||||||| ||  ||||||| ||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gttagattcccatgtttggatga--gcaatga-atttctgct--gctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| |  || |      || ||||  ||||  |  |   || |  |   | |||   | || |  |  | |  |||  | ||   ||||| |||||| ||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||| | |||||| ||||||||||||||||
gtgaagtttcgtaacctgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
---------------------gttag--attcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctc-ttttttttttggc----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                     || |   |||      | |   ||  ||||| ||  |   |  |||  |  |    |  |||||   | | | ||  ||||     ||| | |||||||||||||||||||| ||||||||||| || ||||||||||||| |||||||||||||||  | ||  ||||||| || |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagcca--aactgatccatgtgttacttggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
gttagat-tcccatgtttggatgagcaatgaat---ttctgctgctttatcaa--------------gttatagtaa--ctggctcttttttttttggc-----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| |  | | |||||||  ||| |  |||  ||   |  |  |||   || ||              | |  |  ||  |||   | | | ||  |        ||| | |||||||||||||||||||| |||||||| || || ||||||||||||| |||||||||||||||  | ||  ||||||| || |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
gttagattcccatgtttggatgagcaatga--atttctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| | |||| |     || || |  ||  |  |       || |  |  ||  ||  |||| |   |  | |   |     ||||| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| ||||||| |||||  |
gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 10
gttagattccc--atgtttggatgagcaatgaatttctgctgctttatcaagt----tatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| |  || |      | || ||||| |   ||   | |   |  ||||   |    | |  || |  |       | |||||  ||||||||||||||||| || || |||||||||||||| || |||||||| || || || || |||||| | | |||| ||||||| ||||| ||
gtgaattttcttatcatctgaatgagaatgaaagagccgtatcaatatctgctgtaatctgatagcgtgggtaacatcttttg--cagCTTTGTGATTTATACGAGAACGATTCAATTTTTGACAAATTTGAGTGCTGCCTCAGCGGCGATGGACTCCATGTTGCAACTGGTTCTTATAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
gttagattccca-tgtttggatgagcaatgaattt------ctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| || |||| | | ||| || |||  ||  ||||       || ||||||    | |  || |  ||   |  |  ||||     ||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||| |||||||  |||| ||||| |   | || || ||||||||
gtcagtttcctaatattttga-gagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcatttt-----cagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| |||    | | | ||    | |  | | ||  || | || | |  |    ||   ||  | | | ||||    ||   ||||| || ||| ||||||||||||| || || |||||||| |||||||||||||| ||||| ||||||||| | ||  |||| || ||||||||
gtgagagcttc-tttctgtggcatcttttatttgttgattctgtgttgaaagctaaccac--gttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gttagattcccatgtttggatgag-----caatgaatttctgctgctttat------caagttatagtaactggctcttttttt---tttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
|| || || |  |  |  ||  ||     ||  |||   || || | |||       || | ||   | ||   || ||| |||   | |  |||| | |||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||| |||||||  | || || ||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattactctctgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctctttttttt---ttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                 ||||          | | ||   || ||||  ||||| | ||  | ||  | |  | ||    | | |||| |   ||   |||||||||||| | || || || || || ||||| || ||||||||||||||||| ||||| |||||   ||||||| ||||||| ||||||||
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcag-ttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaac-tggctcttttttttttggc--cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                 ||    |   ||  |||| |  | | | ||  || || | |   |     | || |||  |   |  |||| | | |    |||||||  |||||||| |||||||| || ||||| || ||||||||||||||||| ||||| |||||  |||||||  | ||||| || |||||
atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgc-tgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

upper sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
----------------------gttagattcccatgtttggatgagcaatgaatttctgctgctt-tatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                      |  |||         || | || |  |||  ||| ||  | || |||  |  |     || |  ||    ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  ||||||| || |||||
cttcaatcaaaatataactgaaggcagaacaggggaattagttg-gttatg--tttgtgtcgtttgtattgaactcacagaaattacttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

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|298194583|gb|HO043055.1|HO043055
EST:     ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
genomic: ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
EST: gi|193311638|gb|FK275534.1|FK275534
EST:     TTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
genomic: TTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTA-TTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
EST: gi|14990248|gb|BI315921.1|BI315921
EST:     ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
genomic: ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
EST: gi|208333147|gb|GE128194.1|GE128194
EST:     ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGAT
genomic: ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGAT
EST: gi|254342009|gb|GR853146.1|GR853146
EST:     ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
genomic: ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
EST: gi|207842807|gb|GD817319.1|GD817319
EST:     ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG                         CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT
genomic: ATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGgttagattcc ... ttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
                          tagtaac  putative branch site (score: 1)
                                ctggctcttttttttt  CT-rich tract
              tttatcaagttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattcccatgtttggatgagcaatgaatttctgctgctttatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA