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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT

Basic information

species Zea mays
transcript GRMZM2G017845_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttctt-ttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                         |  |||  |   | |||  | |   || | | ||    ||   ||   |  |   |||||  |  || | |||     |||| |          || |||||| |||||||||||||||||||||||||||| ||||||||||| ||||||||||||||| |||||||||||||||| ||||||||  |||| |||||||| || ||||
-----------------------------------------------------------------------aataattg-acatgtgaaagttgttaaca-tgtgttaagtaaca-gccgacaatttctttttgtttttttaaatgcgccatcttac--------agttccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttctt--ttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                         |  || |   | || ||  | ||  |  ||| |||          | | || |  ||  |  | || || ||     | |     |||     |||  |  |   ||||||| ||  |||||     |||||| ||||| ||||| |||||||||||||||  ||||||||| ||||| || |||||    |||||||||||  | || |
-------------------------------------------------------------------------tcctttttgaattacaaattgtccgctttattttg---------ttctttcaattttgctagttatagatataca-gcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                          | || ||  || || |  |   |  ||  | |       |   |||   |   || | ||||        ||||   | ||| |||||| |    | || ||  |||||||| ||||||     ||| ||||||||||||||||||||||| |||||| | || ||||| || ||| | || |||   ||||||||| |  | || |
-----------------------------------------------------------------------ttagattttg--aaaaagacatgcttttaagttttcacc---ttgacttcaaccttatatctcattgcctgt-tgttggtttttggtaatatat----attttttcacagATTCCAACAAATCCTGCTGGTCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCACGAACATGATGGTACTACACGCTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtt-tactcttgctaatatctgattact--tcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                       | | ||||   |  || ||| |  |  |  ||| |       ||| |||||  |   ||| |  | || || ||    |||  |||  |||   |||||  |  || || ||||||||  |||||     ||| || ||||| ||||| ||||||||||||||| |||||||||| ||||| || |||||    |||||||||||  | || |
-----------------------------------------------------------------------cttttttgaatt--tagaat-tgcccactttattt-------tgttctttcaat-tttttctagttatagatataaagtacaattg--aatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaa--taaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                        ||   ||  |  |  | || | |   |    | | |   | ||  ||        | || ||      |  ||  |            |||   || ||  ||| ||  |||| || || |||     |||||| ||||| ||||| || |||||||||||| ||||||||||||| || ||||||||  | ||||| ||| |  | || |
-----------------------------------------------------------------------tcttcatgaacagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactag------------aattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttca-tgattgacatgtt-tactcttgctaatatctgattact--tcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                        |  ||| ||  ||| | |  | ||  |  ||| |||          | | || || ||||  | | || || ||    |||  |||  |||   |||||  |  || || ||||||||  |||||     ||| || ||||| ||||| ||||||||||||||| |||||||||| ||||| || |||||    |||||||||||  | || |
------------------------------------------------------------------------ccttttttg--aattagaattgtccactttattttg---------ttctttcaactttttctagttatagatataaagtacaattg--aatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 3
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                   |||    |      |    |   |   | | ||| |      | ||||    |    |||||| ||||   |  ||  |            |||   || ||  ||| ||  |||| || || |||     ||| || ||||| ||||| || |||||||||||| ||||||||||||| || ||||||||  | ||||| |||||  | || |
-------------------------------------------------------------------cttcatagaacaaaccttaagtttgccttttcaaaaaagaaaaaaatggcagtaagatacattgttca--gtaaactag------------aattattggttctttccttgtagATCCCAACTAATTCATCTGGTCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 5
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT-
                                                                         |  ||||  |  |||     || |   || | |   |  |  |||||  |     ||   | | |      ||||   | ||| |||||| |    | || ||  |||||||| ||||||     ||| ||||||||||||||||||||||| |||||| | || ||||| || ||| | ||||||   |||||||||||  | || | 
-------------------------------------------------------------------------taattgtttt--taactctcatgttagat-tttaaaaagacatgcttg-taagttttcaccttaacctgt-tgttggtttttggtaatatat----attttttcacagaTTCCAACAAATCCTGCTGGTCTTATTGAATATAGGGCACATCCATTCTGGATCCAGAAATATTGCCCTACTCATGAACATGATGGTACTCCACGCTGTTG

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT1G19270.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaat-gtgctttctct-acatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                   |  ||  | |  ||| |||  || |   |       | |  ||| | || | | |||  |  | || |    ||| ||| || || |   |  | |  ||  |||  | ||| |   | | ||| |   ||||| || ||||||     ||| |||||||||||||||||||||||||| ||||| || || || |||||||| || |||   |||| ||| ||||| || |
--------------------------------------------------gtacgtaaacctctttccttttctatcattttagcccataaatatattca-tgtgttgttgttttgttccggatcttacacttatcgtctgttgctttgtttttctcccgaatgt--aaattctt-tgaacagATACCAACAAATCATGCTGGTCTTATTGAATATAGGGCACATCCTTTTTGGGTTCAGAAGTATTGTCCTTCTCACGAACACGATGCTACCCCGAGATGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                     ||  || | |  | | |    |  ||||| | ||| ||    ||  |   ||| |    | |   | | || |  ||| |     |   |||      | ||| || |  ||||||| ||||||     ||| |||||||| |||||||||||||| || ||| | ||||| || ||||||||||||||    ||||| |||||  |||| |
--------------------------------------------------------------------gtgagtgatagc-caacttctgttgatctcta-tattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatg----tataaat-----gtaactcctct--agATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT

upper sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 6
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatct-atctccaatatcttggagaatgtgctttctc-tacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                                                                   || |||||   || | |||| |       | | | | ||    ||| |   ||||  |     ||| |    ||  |   |  | | ||  | ||| |||||||| || ||      ||| ||||||||||||||||| |||||||| ||||| || || ||||| ||||| |||||    ||  | || || || ||||
-----------------------------------------------------------------------------------aagaaaatgagatatgcaattttactactattcttcctttggatacttcactcattttcagtttgtgttggtttcttggaacataaatatatttttacagATTCCAACGAACCCTGCTGGTCTTATTGAATATAGGGCGCATCCTTTTTGGGTTCAGAAGTACTGCCCTTCTCATGAGCATGACAGAACACCTAGATGCT

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|211158047|gb|FL160652.1|FL160652
EST:     CTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGGTC                         ATTCCTACAAAAATGA-TGGCCCTTATGGA-TAAAGGGCCCTTCCTTTCTG
genomic: CTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatca ... ttcttttcagATTCCTACAAATATGAATGGCC-TTATTGAATATAGGGCACATCCTTTCTG




















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: 48 (upstream exon), 47 (downstream exon)
Score: 60

TTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatca ... ttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 89

TTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatca ... ttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 90

TTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatca ... ttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

TTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatca ... ttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
                                         ttacttcttttc  CT-rich tract
                               taatatct  TA-rich tract