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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

Basic information

species Zea mays
transcript GRMZM5G871463_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
-------------------gtatgaagctcctcaacccttccattgctgg--ctgtcccttttac------tgtgcatgcatttttagcttgcttgtga-tgattgggttgtctattt----tctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
                   ||      | | |   ||  | || || |||   ||| |  ||| |      |||       ||  | |||   | ||   || ||| ||| ||| |||    | ||| ||| || ||||| ||||||||||| |||||||| ||||| |||||||||||||||||||  |||||| ||||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttctgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggtt-gtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
   | |   |  |      ||   | |   | |     | | | |||      ||  |  | ||  || || ||||| |||| |  | | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||
--gtaagtttatttctgttttttttagtgagataatgttgtaagtgtttgaa-atggtgggttttgttttgttgatttggttcggttttgtggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctg-------gctgtcccttttactgtgcatgc-----atttttagcttgcttgtgatgattgggtt-gtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG-------------------------------
   | |   |  | |   ||    || |||       | |||   || |  | |   ||      ||  |  | ||  || || |||||  ||| |  | | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||                               
--gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtccctttt---actgtgcatgcatttttagcttgcttgtgatgattgggttgtctatttt---ctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
      || |  |  |   |     ||  |  | |   ||||   ||||     || ||| |   || ||| |  |||     || | |  |||    | | |||||||||||||||||||||||| || ||||| ||||| |||||||| || || || |  |||||| | ||
-----gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctg-------gctgtcccttttactgtgcatgc-----atttttagcttgcttgtgatgattgggtt-gtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
   | |   |  | |   ||    || |||       | |||   || |  | |   ||      ||  |  | ||  || || |||||  ||| |  | | |  | | |||||||||||| || |||||||| || ||||| |||||||||||||||||||| || |  |||||| | ||
--gtaagtttttttatttctgtttttactgagataatggtgttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtatgaagctcctcaaccctt--ccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
| | |    |  |          ||   |  || |     ||||  | |   ||        |   |   | |  |  |   |||  | | |  | | |||||||||||||||||||||||| || ||||| ||||| |||||||| || || || |  |||||| | ||
ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtt-tgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
||| | || |    |    |   ||          || | ||| |         ||    | ||  || |      |||||||| | ||   ||| |||||| ||||||||||| ||||| ||||| || || || |||||||||||||| || |  |||||  ||||
gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgt-tgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtatgaagctcctcaacccttcc--attgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
   |||   |         | |   |||| ||  ||    ||  | ||| |  | |||  | |  || |    |   |||  || | |||      | ||||||||||||||| |||||||| || ||||| ||||| || ||||| |||||||| |  |||||| ||||
--gtgagtttgagttgttttgctggattgatgattgatgattg-aatgtactggtattcgtgggctgatgaatacttttgaattttgtat------tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgct-tgtgatgattgggttgtctattttctctcaa---gGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
                                 ||    || ||   ||   || |||    |  || | | ||| |    || | |   ||  |  ||   |||| ||||| || |||||||| |||||||| ||||| || ||||||||||| || |  |||||  ||||
---------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgcggaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctc---aagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
|| |     |  || | | |  | || ||  || |   | |   ||||   | | || |   |    | |  || |            ||| |  |   |||||||||||||||||||||||| ||||| || || ||  | ||||| ||||||||  | |||||| | ||
gtctcgttgtgttcgaacttctctttcct--ctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgct-tgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
                                 ||    || ||   ||   || |||    |  || | | ||| |    || | |   ||      ||||| ||||| || |||||||| |||||||| ||||| || ||||||||||| || |  |||||  ||||
---------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|211293088|gb|FL433983.1|FL433983
EST:     TTCGAGTACAGGGCGGCCACGGGTTGGTTCACCCCTGACGGCGTGGCAGT                         GTATGGCAAATGTGAGATGCGGTACAACCCGGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|26456797|gb|CA828380.1|CA828380
EST:     TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|161591399|gb|EY962234.1|EY962234
EST:     CGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGT
genomic: CGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGT
EST: gi|211485856|gb|FL429903.1|FL429903
EST:     TCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGNCAGT                         GTATAGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATG
genomic: TCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGG-CAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATG
EST: gi|37379451|gb|CF626469.1|CF626469
EST:     TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|60355176|gb|DN222149.1|DN222149
EST:     TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|211492877|gb|FL137487.1|FL137487
EST:     TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|78544163|gb|DV621661.1|DV621661
EST:     TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
EST: gi|5152847|gb|AI759012.1|AI759012
EST:     TCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGT                         GTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG
genomic: TCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 116

AGAACTATACCAGGCTTGACAATGTTGGGCCTGAGGACTTCTTCTGCCGATTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

AGAACTATACCAGGCTTGACAATGTTGGGCCTGAGGACTTCTTCTGCCGATTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 72

AGAACTATACCAGGCTTGACAATGTTGGGCCTGAGGACTTCTTCTGCCGATTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 63

AGAACTATACCAGGCTTGACAATGTTGGGCCTGAGGACTTCTTCTGCCGATTCGAGTACAAGGCGGCCACCGGTTCGTTCACCCCTGACCGCGTGGCAGTgtatgaagct ... ttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctcaagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG
                                    ttgtctattttctctc  CT-rich tract
         attttta  TA-rich tract