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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA

Basic information

species Zea mays
transcript GRMZM2G176546_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                            |||  | |||||| |  || | ||  |||  ||     | ||||||  ||| |    |||||||  || ||| | | ||    || |||||  |    |  ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || ||||||
-----------------------------------------------------------attttttaggctatctattttaatt-tattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttctttt---ctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 17
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaat---ttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                        ||| ||| ||| | ||        |||||      ||     |  | |||||||| |    |||||||  || || | | ||   || | |   || |  |||  |  ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |  ||||||
--------------------------------------------------------cacattttcttaggta--------atttaagcc--cctggaactgtatttgatctgattagttttcttattaaataaattattaattgattgtgttttaatggtctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacactt--ttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                       || | |  |  | || |||  || |      || ||||    |  |  ||  |||  |   |     | ||  |  |  ||||     ||               |||||||| ||||| || || ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||||||||| ||  | || || || ||| ||
------------------------------------------------caatgacacccctagtatcctgtctactttctcagcccacttttta---aaacattgactgaatttgtcaagcatattaatgaaagattaccattttg--------------tttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctgg-attttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                      ||       ||| |      |||    | ||| || ||       | | |      |   | |  ||  ||    || || ||||    ||  ||  | ||   || |||||| ||||| || || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| ||  | || ||||| ||| ||
------------------------------------------------------aatgacacccctag------ttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcat-atgaatga---aagcttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattt---tagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                    ||        | |   ||| || | |||  |||||||||     ||  ||  ||| | ||    ||||   ||    || ||   ||  | ||||||        |||   ||| || |||||||| ||||| || || || || || || |||||||||||||| |||||||| ||||||||||||||||| ||  | | ||| || || |||
----------------------------------------------------agggag----tgcaaagctctagtcttgggttacatttt----ggggacttgttggtatc----ttttgaatcgcgaatcatc--tgagtgaaattttctgatcctttgaatagAAAGAAGAACATCTTCAAATTGGCGCAGGGGGAGTATATAGCTCCAGAGAAAATTGAAAACGTCTATGCCAAATGCAAATTTGTGGGCCAGTGCTTCATA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                                        | || |  ||  | |  |||     |   | | |    |  | |          |  | | ||  ||    || ||     || ||   ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||| |||||||| ||| ||||||| |  ||| || | || ||||| || 
-----------------------------------------------------------------------gttttataaatcaaaacattctt---gttatttctttctttgcggaagaaaaagttgaaatgtt--tgttaaaacttcaatgtgcatgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                             | ||| || || |   ||  |       |          ||||     ||    | | |   || | |  || | |   |  | |||    ||| |   || ||       ||   |||||||||||||| |||||| | || || || ||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||  || ||||||||||||| 
------------------------------------------aattgcttacaaaagaaactttgtgaagagcagga-------acatgccaactttaagttatgaaatttta--gtctcttagcgaaaatt---gatggcc--aactt-------atgacagGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
-----------------------gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttctt------gcagaacactttt-ccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtt-tttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                       |  |   | |  ||   || ||| |   |||  ||     |||  |   |       | | |   |  |  |||||   | |  ||   |||    |    | | |  |  ||     |  | ||   | | | | | |||    ||  |||||  | |  |  ||   ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||| ||||| ||||| |||||||| ||  ||||||| || ||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagt-tgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                         | | |||  ||    | |   |     | ||| ||   | | |    ||  | |   | | ||| ||  | |||        |||| |||  ||    |  |  ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||| ||  | |||       |   ||| ||| | || |||||  ||
--------------------------------------------------aagttttattcttctctgaaactgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtttgttt-tgtat--------cctttaatcact----gtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                                                                                | |||  ||  |   ||   |||  ||| | |  |   |  | |     ||||||||||||||||| ||| | || || || ||||||||||| |||||||||||||| |||||||||   ||| |||||||| |||| || |||||  | 
--------------------------------------------------------------------------------------------------------------gtaacgtgctttgtgtcattcgattt-tgcttgacgtcattttttg---ccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                                                                                                                | |||  ||  |   ||   |||  ||| | |  |   |  | |     ||||||||||||||||| ||| | || || || ||||||||||| |||||||||||||| |||||||||   ||| |||||||| |||| || |||||  | 
--------------------------------------------------------------------------------------------------------------gtaacgtgctttgtgtcattcgattt-tgcttgacgtcattttttg---ccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|6194573|gb|AW146677.1|AW146677
EST:     GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|67023162|gb|CO451911.1|CO451911
EST:     GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATTGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|6194494|gb|AW146598.1|AW146598
EST:     GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG                         GAAAAAGAACATTTTCTTGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|50335868|gb|CO530994.1|CO530994
EST:     GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA

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: 40

AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

AAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAGgtaaaaacgt ... tggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
                       tattaat  putative branch site (score: 66)
                                      tttctcct  putative PPT
                  tatattattaatgcct  TA-rich tract