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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 1
gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
|||||  |||| |    ||  ||   || |||  |   || |||||   |     | ||| |    |  | |||  |||  |  |  |||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| |||||||||
gtaagc-atcctccccgccttccttccttccttccttccttccgccaccacc--atcctcaccctcctcctccgcctcc--cgcc--cgcagTTCAACGTCCCCGATCTCCGCGTCGGCACGCTCGACTCCCTCCTCGCCCTCAGCGACGATCTCGTCAAG

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 1
gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
||||    |    | |  | |      |     | ||| || |       |    ||| | ||| |  ||  | | ||  |   || ||||||||||| | ||  | ||||||||||| ||||| ||||| || ||| |||||||||| ||||||| ||||
gtaattactaatatataacaataataataataattactttctc-------tgctattcgctcgttga-tcttcttctcttctggct-cgcagTTCAACATTCCCAACCTCCGCGTCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G26220.1 (Glycine max), 3'ss of exon 1
gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttc-------------------tcgcgtcgcctcaccgtat----------------ccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
       |  | || |  |   | ||||| ||||| ||||| |  |  | |||  ||                     |||||| | ||    | |                || |||  | ||||||||||  ||||  ||||||| ||||| ||||| ||||| || ||| ||||||||||||| |||||||||
-----gtactctctctctctctctctctctctctctctctcacatcacatttttttttataaccaacaaaacaaccaccgcgtctcttccttttcttctcattttcattttccctccaaattcgcagTTCAATATCCCCAATCTCCGGGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATCTCGTCAAG

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 1
gtaagagatccccttttccgacccctctccctctcactctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
    |  || |  |||         |     || ||||||| | | |  ||||   | | |         | | | | |  |     ||||||||||| ||||  | |||||| |||| ||||| ||||| || ||| |||||||||| ||||||| ||||
----gtaattctatttataa-----taataatcacactctctctctgctatttgcctattg---------atcttcttcttctctgtcgcagTTCAACATCCCCAACCTCCGCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 1
gtaagagatccccttttccg-acccctctccctctcactctcccgccggaatttagt-tctcgcgtcgcctcaccgtatccg-ccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
|||||   || |  | ||   ||  | ||   | |   |  ||  |    |    |  |||  | |  |||| |  | |||  |||  | ||||||||||| ||||  ||||||||||||| ||||| ||||| || ||| |||||||||||||   |||||||
gtaagtactctctctctctacacatcactttttttttataaccaacgaccaccgcgcctcttacttttcctctcattttccctccaaattcgcagTTCAACATCCCCAATCTCCGCGTCGGAACCCTAGACTCCCTCCTCTCCCTCAGCGACGATACCGTCAAG

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|211396453|gb|FL097334.1|FL097334
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396451|gb|FL097332.1|FL097332
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|71428528|gb|DR809578.1|DR809578
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396449|gb|FL097330.1|FL097330
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396455|gb|FL097336.1|FL097336
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|13177876|gb|BG349059.1|BG349059
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211419024|gb|FL311427.1|FL311427
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396448|gb|FL097329.1|FL097329
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|9824919|gb|BE575016.1|BE575016
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396452|gb|FL097333.1|FL097333
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|116818640|gb|EC861688.1|EC861688
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396454|gb|FL097335.1|FL097335
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|211396456|gb|FL097337.1|FL097337
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|15312777|gb|BI478368.1|BI478368
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
EST: gi|21987710|gb|BQ779238.1|BQ779238
EST:     GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGC                         TTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC
genomic: GCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTC

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: 187

GTCTCTGCCCGTGCAGTCACCTGGCGCCATCGCAAGCTCCCTGTGGTCTCGCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 247

GTCTCTGCCCGTGCAGTCACCTGGCGCCATCGCAAGCTCCCTGTGGTCTCGCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GTCTCTGCCCGTGCAGTCACCTGGCGCCATCGCAAGCTCCCTGTGGTCTCGCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 187

GTCTCTGCCCGTGCAGTCACCTGGCGCCATCGCAAGCTCCCTGTGGTCTCGCCTCCAGGACTCCATCTCCCGCCACTCCTTCGACACTCCGCTCTACCGCgtaagagatc ... atctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcccgccggaatttagttctcgcgtcgcctcaccgtatccgccatctgcgcagTTCAACGTCCCGGATCTCCGCGTCGGCACCCTCGACTCGCTTCTCGCCCTCAGCGACGACCTCGTCAAG
                            gcctcac  putative branch site (score: 187)
           aatttagtt  TA-rich tract