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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttccaagaacacttgaatctatccttgttttccagttatttctatgctcactgtcacctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG

Basic information

species Zea mays
transcript GRMZM2G154165_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 3
--------------------------------gtaacatttccaagaaca-cttgaatctatccttgttttccagttatttctatgctcac--tgtcacct----gcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG
                                 |    ||| |  |   |  || ||    |  |||||      || |   |||  |  |  ||| ||||      ||  |||||||| || || ||||| |||||||| ||||||||||||||||||||  | || || || ||  |||||||
gtaagttgatggtgtttatattgaaatagtttttcctctttacttgcgtagtttaaacaggttgttgttaaatgtttctggatataatgtccgtgttacctttccatttcaagGTATCCCCTCGGTCGTGTAATTGGTGGGACTGTCTATCCTGGTTTGACGTTGACAGCAGGCACCTTATGGTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 3
----------------------gtaaca--tttccaagaacacttg---aatctatccttgtt-ttccagttatttct----atgctcactgtcacct----gcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG
                      | ||||  ||| |    | |||||   | | ||  |  ||| ||     | |||||    ||  |  |||| ||||      ||  |||||||| ||||| ||||| |||||||| ||||||||||||||||||||  | || || || ||  ||||| |
gtaagttgatggtgtttatattgaaacactttttcctctatacttgcatagtttaaacaggttgttgttaatgtttctggatataatgtctgttacctttccatttcaagGTATCCCCTTGGTCGTGTAATTGGTGGGACTGTCTATCCTGGTTTGACCTTGACAGCAGGCACCTTATGGCG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaacatttccaagaacac--ttgaatctatccttgttttcc---agttatttct-atgctcactgtc--acctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG
                      |  |  ||     || ||   |||     |   |   |||||   |||| ||  | |   |  ||||   || | | || |||||||||||||| ||||| |||||||||||||| || || || |||||  | || || ||  | ||||||||
gtaatcattattaaaactgtccgatatgttctggtgaccatgtttgtgctcacgttatctttccttaagttgttaatgacagtatctgttctacttccattaagGTATCCTCTTGGTCGTGTGATTGGTGGCACTGTTTACCCAGGATTGACCTTAACAGCAGGCTCCATATGGTG

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|71447978|gb|DR829028.1|DR829028
EST:     TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATG                         GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACT
genomic: TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACT
EST: gi|93015443|gb|EB640963.1|EB640963
EST:     TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATG                         GTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACT
genomic: TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACT
EST: gi|71447977|gb|DR829027.1|DR829027
EST:     TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATG                         GAATCCTCTTGGGCGTGTTATTGGAGGGACTGTCTATCCTGGTTTGACACT
genomic: TCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACT

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: 120

TTCTTGTCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG


Block sizes: 43 (upstream exon), 28 (downstream exon)
Score: 2

TTCTTGTCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 10

TTCTTGTCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

TTCTTGTCAAAGAATGGCATATATGAATTCTGGAACTGGTTTGATGACCGAACATGgtaacatttc ... ctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatctatccttgttttccagttatttctatgctcactgtcacctgcttttagGTATCCTCTTGGGCGTGTTATTGGTGGCACTGTCTATCCTGGTTTGACACTTACTGCTGGTACAATATGGTG
                                tgctcac  putative branch site (score: 32)
                                            cctgctttt  putative PPT
                       ttatttctat  TA-rich tract