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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggaatgctaaacgccacatgttaatgaatgataccctttgtagttatgccaattattgactcatatatatgctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC

Basic information

species Zea mays
transcript GRMZM2G142111_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142111_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g34940.1 (Oryza sativa), 3'ss of exon 2
------gtggaatgcta-aacgccacatgttaatgaatgataccctttgtagttatgcca-attattgactcatatatatgctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
       || ||| | | || |  |   | ||||    |||| || |    |||| |  |    ||   || || ||    ||    ||||||||||||||||||| |||||||||||||||||||||||||||||| || || ||||| ||||||||||| |||||||||||||| |||  |||
gtaaatttgcaattccataatgtaatcagataatattggatatccctcactgttacgatatgccatgtgctgatctacgccct---ccctgagcagAGAAGGATTGTTGGTCTCCATCAGAATACCTCTATTGAATCAATCGACATAACTGACACTTGGGAACCATTGGAAGAAGGGCTTAACAC

upper sequence: GRMZM2G142111_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39480.1 (Glycine max), 3'ss of exon 3
gtggaatgctaaacgccacatgttaatgaatgataccctttgtagttatgcca-attattgactcatatatatgctatatcctgag-cagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
|||| | | | ||   |       |||   |    |    | |  | ||   |  ||  ||  |  |     | || |  | ||   ||||||||||||| |||||| ||||| || |||   |||| ||| | ||||||||| ||||| ||||| ||| | |||||||||||| |  |
gtgggaggatcaatatctttatggaatatgttggcctgcatttgttcatcttatgttcatgtgttgtgatggttctgttccttgtttcagAGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC

upper sequence: GRMZM2G142111_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G15380.2 (Glycine max), 3'ss of exon 3
gtggaatgctaaacgccacatgttaatgaatgataccctttg--tagttatgccaattat-tgactcatatatatgctatatcctgag-cagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
|||| | | | ||   |   |  |     ||| |  |||     |  | ||   | ||   ||| |  |     | || |  | ||   ||||||||||||| |||||| ||||| || |||   |||| ||| | ||||||||| ||||| ||||| ||| | |||||||||||| |  |
gtgggaggatcaatatc--tttatggaatatggtggcctgcacttgttcatcttactttcgtgagttgtgatggttctgttacttgtttcagAGAAGGATTGTTGGTCTGCATCAAAACACCCAAATTGGATCAACTGATATAACTGACACATGGGAACCACTAGAAGAAGGCCTTCTTCC

upper sequence: GRMZM2G142111_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0072g00330.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtggaatgctaa-acgccacatgttaatgaatgataccctttgtagt-tatgccaattattgactcatatatat-gctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
                            ||  |  ||| | |   ||| ||   | ||  |||  |||||  | ||||  |  |||   ||| |  | ||   | | ||     ||||||||||||||||||||||||||||| || || ||||  || | ||||||||| || |  ||||||||| | |||||||||||| |  |
gtaaccaacattatttgcctattttttcggtctattaacatgggtcattttgg-gtatattactttttgttatatatgtta--tatatgctcgttaacattagtttctctcattcagAGAAGGATTGCTGGTCTCCATCAGAACACATCGATTGGTTCTACTGATATAACTGATATGTGGGAGCCACTAGAAGAAGGCCTTCTTCC

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|78122944|gb|DV541328.1|DV541328
EST:     CCGTGGGAGGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGGTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|91874466|gb|EB404423.1|EB404423
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|71435668|gb|DR816718.1|DR816718
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211038564|gb|FL344525.1|FL344525
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|83278985|gb|DV942993.1|DV942993
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211006797|gb|FL317956.1|FL317956
EST:     CATGGGTATGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCYTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTG
genomic: CATGGGAA-GGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTG
EST: gi|211470848|gb|FL358523.1|FL358523
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211116607|gb|FL350319.1|FL350319
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211312453|gb|FL348221.1|FL348221
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATA
EST: gi|211401785|gb|FL336222.1|FL336222
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211442302|gb|FL322986.1|FL322986
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
EST: gi|211442303|gb|FL322987.1|FL322987
EST:     CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAG                         AGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA
genomic: CCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATA

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: 49 (upstream exon), 49 (downstream exon)
Score: 126

GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 62

GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GACAATGCAACAGATGACATTGTCATCAAGGCCATGGGAAGGGCGATCAACAAGACAGTTGCCATCGTGGAGCTTCTTAAGgtggaatgct ... tcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccctttgtagttatgccaattattgactcatatatatgctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC
                      tattgac  putative branch site (score: 161)
                               atatatatgctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggaatgctaaacgccacatgttaatgaatgataccctttgtagttatgccaattattgactcatatatatgctatatcctgagcagAGAAGGATTGCTGGTCTCCATCAGAATACCTCTATTGAATCCATTGATATAACAGACACTTGGGAGCCATTGGAAGAAGGCCTTGTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG