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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT

Basic information

species Zea mays
transcript GRMZM2G143747_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
gtatgcacaacgcgtctctcgttgcattaattagcaa------gcaagcattgtgaccatgg-cagctgggttcgtcgctgtgctgaacacgatttttgt----tttggttc----ttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
|||||||| |  |  |  ||    | || || |  |       || | || ||  |   ||  ||  | | |  |  | | || |||    | || |  |    |    | |     ||| ||||||   | | |   ||||| || || || ||||| || || || ||||| ||||| || ||||| ||  |||| |||||||||||||||||||||||||||||| ||||  | ||||
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                              | |||     | |  | |    |    || |  |||  || || | || | |   |||   |||     |  || |||||   |        ||||||||| || || ||||||||||| || ||||| ||||| |||||||||||  | ||||||||||| || || || |||||||||||| ||||| | || |
-----------------------------gtaagcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaatt-----atacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 1
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                                     | |||  |    ||  |   |  |  |||          |  ||     || | ||  | ||| |  | | |  |||         |||||||| || || ||||||||||| || ||||| ||||| |||||||||||  | ||||||||||| || || || |||||||||||| ||||| | || |
-------------------------------------gtaagtttaagaactcttttactttagtttact----cacccaaattctttctagtcctagttttcatgt-tgatgttaaattatgcagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------gtatgcacaacgcgtctctcgttgcatt-aattagcaagcaagcattgtgaccatggcagctgggttc---------gtcgctgtgctgaacacgatttttgttttg----gttctt-ttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                                                          | |   | ||  |  | |   |  ||| |   | ||    || |   |  | || | | |||  |||           ||  ||    ||||   ||  |||||      || ||   ||   | | |   |  |  |||||| | || |||||||| ||||||||||| || ||||| ||||| || ||  | || ||||| ||||||||||| |||||| ||||| |  |  | ||||
gtatgtctctccctctctgtctctctctttctagattttgtttccgacattgttgctctgttttccacttgattttgagtttattcagacaacatttcagtaaattagctatag-atctgttttccgttcagacaacgtcgtcaccaacattgttcgtgtttcatacagtactaactagaatcttttgtgttgatcagGTGAATCTGGTCGGAGGTTACTACGACGCCGGAGACAATGTGAAATTTGGATTACCGATGGCTTTCACGGTGACGATGATGGCGTGGAGTGTGATTGAGT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23398 (Selaginella moellendorffii), 3'ss of exon 1
-----------------gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttt-----tggttcttttatgttttgtctcgccgga-------cagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                 |  |  || |    |   | |||       | | ||  |     || |   ||  | ||  |  ||| ||||  |       |   ||  |  |      |||   |||  |    || | |||           ||||| || |||   ||||| |||||||| || ||||||||||| ||||| || || |||||||| |||||| | || ||| | |||||| || |  | ||||
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcatccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgacccgcaatctttgttccagGTTGATCTCTCGGGAGGCTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ25378 (Selaginella moellendorffii), 3'ss of exon 1
-----------------gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttt-----tggttcttttatgttttgtctcgccgga-------cagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                 |  |  || |    |   | |||       | | ||  |     || |   ||  | ||  |  ||| ||||  |       |   ||  |  |      |||   |||  |    || |||||           ||||| || |||   ||||| |||||||| || ||||||||||| ||||| || || |||||||| |||||| | || ||| | |||||| || |  | ||||
gtacgaaaagctctcaagattctaccatcttttctttgttcttcgtttcatcacccctttgttcttcgcaaagtagacgatttcctcgcattctctcttagttttccttctcaaaggtggagttttccttcactgactcgcaatctttgttccagGTTGATCTCTCGGGAGGTTACTACGATGCCGGCGACAACGTCAAGTTTGGACTCCCCATGGCCTTCACGATCACGATGCTCTCGTGGAGCGTGGTCGAGT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcat-tgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                         |   |   |||  | || || | |  || |  | | || |  | | || |   |||  ||  |||  ||| ||||  ||    ||   |      |   ||||||||  | || |||||||| |||||||| |||||||| || ||||| |||||||||||||| |||||  | ||||||||||||||| ||  | | ||||
-----------------------atagatagctgcattcgaggatatctttccctttcggatgtgc-ctttgc-gaattgagtac--tttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

upper sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ13916 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                           ||  ||||        |   |  |  |  |    || |  | |  || |          |||  ||| ||||  ||    ||   |      |   ||||||||  | || |||||||| |||||||| |||||||| || ||||| || ||||||||||| |||||  | ||||||||||||||| ||  | | ||||
--------------------------gtagatagctgcattctaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactaccagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGTCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

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|37418691|gb|CF647017.1|CF647017
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
EST: gi|76927311|gb|DV171235.1|DV171235
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
EST: gi|89761270|gb|DY689355.1|DY689355
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
EST: gi|71447399|gb|DR828449.1|DR828449
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
EST: gi|76919541|gb|DV167769.1|DV167769
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
EST: gi|149075805|gb|EE164339.2|EE164339
EST:     GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGA                         GTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC
genomic: GGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 28 (downstream exon)
Score: 8

CATCCTCTACTTCGAGGCGCAGCGGTCCGGCGTGCTCCCGCCCAACCAGAGGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT


Block sizes: 34 (upstream exon), 16 (downstream exon)
Score: 2

CATCCTCTACTTCGAGGCGCAGCGGTCCGGCGTGCTCCCGCCCAACCAGAGGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT


Block sizes: 38 (upstream exon), 16 (downstream exon)
Score: 6

CATCCTCTACTTCGAGGCGCAGCGGTCCGGCGTGCTCCCGCCCAACCAGAGGATCACCTGGAGAGAGAACTCCGGCCTCTTCGATGGAAAGGCCAACGGAgtatgcacaa ... cgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT
                                     ttttgtctc  CT-rich tract
                           ttcttttatgtttt  TA-rich tract