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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT

Basic information

species Zea mays
transcript GRMZM2G026470_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 5
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                            |    ||||| | | | ||||    | || |  |    |   |||| | |    | | | |   |||||            ||||||| || | || ||     |  || ||||||||||||| |||||||||||||| || ||||| |||||| |||| ||  |  | || || ||||| ||||||||||| ||
---------------------------gtacgcctgcttcctca-gctcatacgattgctacattttttatgcttggtattgcac-cttgatttcaa------------ttgttttatt-cttgatcaaa--atctttcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacg-ctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                 |  || |            ||||    |||  |   ||     |   |||| |    |      || |   ||  | |  |      || |||| |||||||||||||||||| | ||||| |||||||| ||| ||||  | |    ||| |  ||||| || |||||||||||
-------------------------------------------------gtaagatccttat----ctcttgtcaaatcaaataactaaggaccaaaactaaagaagc-----ttataaatcgcgtttgg------tttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EDP02064 (Chlamydomonas reinhardtii), 3'ss of exon 3
---------------------gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcg-ctaggtttccgcgcggt---ccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagAC---AAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT-
                     |   ||    |       | |    |||   |   |     ||| || |  ||  |     | || |    ||  | ||    |  | |  |  ||  | | ||     | || |   |     | ||||   |     |    |||   |||||||||||| |||||||||||| |||  |||||||||||   || |  |  |||    | |   || || ||||  | 
gtgcgtacgtgcgggaaaacagggagcctcagggaaaggtgtg-ggatagtgccaagtcggatgaggcgcaactcagcagtagagcagcaagccgagatgtgctgaccacgtccaccaacgagtgctgacgcggcttcgtctgaccgtgctgcagGTTCTTCGAGGACTACAAGAAGAACGAGCACAAGGAGGTGGTCGTGGACGACTTCCTGGGTGCTGAGGAGGCCAAGAAGGTGGTCAAGGACTCGCTG

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                      || |||     || |  ||||  |  |      |    |  || |  |  | |  |||| |  |||| |   ||||    | || ||||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | |||||
------------------------------------------------------gtatcc-ttttgtgccggctgtgtgag------cgtgttggaattttctctct--ttgtctgctttctttaactggagggagtc-agACAAGAAGAACGAGAACAAGACCGTGGCTGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCAT

upper sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacgctcctccct-tcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
                                                              |    | ||  ||   |||  |      | | |          | |  |||| |  |||| |   ||||    | || ||||||||||||||||||||||   ||||| || |||||||||||||| || |     |||    | || |||||| | |||||
--------------------------------------------------------------gtatccttttgtgtgccggctgtgtgagcgtgttggaattttctctctttgtctgctttctttaactggagggagtc-agACAAGAAGAACGAGAACAAGACCGTGGCGGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCAT

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|32831350|gb|CD971028.1|CD971028
EST:     TGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|33098670|gb|CF058630.1|CF058630
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTT
EST: gi|71331881|gb|DR802819.1|DR802819
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTTCTGCCCCGCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCC-GCC
EST: gi|78023075|gb|DV491462.1|DV491462
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTGGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAATGACTTCTTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|28984521|gb|BQ539133.2|BQ539133
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|71331880|gb|DR802818.1|DR802818
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|62550248|gb|DN830668.1|DN830668
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|60400572|gb|DN233379.1|DN233379
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT
EST: gi|78121801|gb|DV540185.1|DV540185
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|5499294|gb|AI855161.1|AI855161
EST:     CGAGCTCTCCCCTCNCCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|60354156|gb|DN221129.1|DN221129
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCG
EST: gi|60344571|gb|DN211544.1|DN211544
EST:     CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTTGAAGACT                         ACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT
genomic: CGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACT

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 4 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 11

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 421

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 53

ATCGCCGTCTGCGCCGACGACCCCGAGTACCGCCACTACAACGACATCAGCGAGCTCTCCCCTCACCGCCTCCAGGAGATCCGCCGCTTCTTCGAAGACTgtacgcgctt ... caaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
         aactgac  putative branch site (score: 53)
                          ttttgttt  TA-rich tract