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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttcatactaatttcttcttggtctatgacatgatttatagtgtatttgtttctcacattctagttgactgtttatataatggtgatgcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA

Basic information

species Glycine max
transcript GLYMA07G10000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------tgacttcatactaatttcttcttggtctatgacatgatttatagtgtatttgtttctcacattctagttgactgtttatataatggtgatgcacttg----tagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA
                                                             | |  |  | | | ||  |  ||  |   |  |   ||  |||    ||||  |  ||  |||| | |      | |||   ||| | |||   |||    ||||    | ||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||||| |||||||| |||||||| |   | ||||||
gtattatgcgccttatgtcctaaatcttttctgtcaaaaccaatcataaatactttggtccttaaatggtgcaagttattatttatttcttatctaaatacata----attttgtaatctgattccaat-attcatctatggtatgttcatgtgtttggtaatagGGAGCAGTTGGTGCCGGCATATGTTCGTCTCCTTCGTGACAATGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
-----------------tgacttcatactaatttcttcttggt--ctatg-acatgatttatagtgtatt-tgttt-ctcacattctagttgactg--tttatataatggtgatgcacttg----tagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA
                 ||| |||| ||  |||  | |  ||   | |||    ||| || | | ||||  |||   | || |  ||  |  | ||  || |    |      |||  |||    |||  | || ||||| ||||| |||||||| || || |||||||||||||||||||| || || || |||||||| |||||||||||||||| |||||| |||
gtattatttgtcctagctgaattca-acctattattgcagggaaaccatgtgtctgaattcttgagtatcatgtaaacccatagccttttcaaatggattaactgtaaatctctgcttttgggattagAGCTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
-----------------tgacttcatactaatttcttcttggtctatgaca------tgatttatagtgtatt-tgttt-ctcaca-----ttctagttgactgtttatataatggtgatgc-acttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA
                 ||| ||||  ||| | |      | | ||  |||      ||| || | | ||||  |||   | || |     ||||| | || |   | ||||    || |        |||  | || ||||| ||||||||||||||||| || || ||||||||||||||||| || || || |||||||| |||||||||||||| | |||||| |||
gtattatttgtgctagctgaattcaacctattattgcagggttgtaaaacatgtatctgaatttttgagtatcatgtaaacccataaccttttctaatggattaactgtatatctatgtttttgggattagAGCTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA

upper sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 6
tgacttcatactaatttcttcttggtctatgacatgatttatagtgtatttgtttctcacattctagttgactgtttat--ataatggtgatgcactt-gtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA
    ||   | |  ||| ||| || ||| || |    ||| ||    |||  ||    |  |  || ||||||  | ||  |||||  |     | || | |||||||| ||||| ||||||||||||||  |||| ||||| ||||||||||||||||| || || ||||| || |||||||| || |||| ||| ||||| 
--tttttggattggtttattcctgatctgtgtc-cattttttaacaaattatttatataattgttatttgacttatgattgataattatttgatattttgcagGTCAGACTTGGTTCCTGCATATGTTCGGTTGCTTCGTGACAATGAGGCTGAAGTACGCATAGCAGCTGCAGGAAAAGTAACAAAATTTTGCCGGATTTTG

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|193619519|gb|FK570799.1|FK570799
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         ATCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|208239870|gb|GE038172.1|GE038172
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|193585901|gb|FK541623.1|FK541623
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|14258560|gb|BG881468.1|BG881468
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|193337883|gb|FK305022.1|FK305022
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|8285673|gb|BE023232.1|BE023232
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|192310534|gb|FG999543.1|FG999543
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGA
EST: gi|208256618|gb|GE054843.1|GE054843
EST:     GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG                         GTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATG
genomic: GCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAGgtaacctttt ... gcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttgtttctcacattctagttgactgtttatataatggtgatgcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA
                         actgtttatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttcatactaatttcttcttggtctatgacatgatttatagtgtatttgtttctcacattctagttgactgtttatataatggtgatgcacttgtagGTCAGAATTGGTCCCTGCATATGTTCGTCTGCTGCGTGATAATGAGGCTGAAGTACGTATTGCTGCTGCTGGGAAAGTAACTAAGTTTTCCCGCATTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-gacttca
- - - - - - - - -cttcttg
- - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggtg