Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcag

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctgg-attcagtttttctagcaaaaattatggttcttacttcttaca-----ttatgtatactaattgctgattttctctttccatgttgcag
|| | || |||||||| ||||| ||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||||| |||| |||||||||||  | ||||  | |||||||| || ||||   || |||||  |  |   |  |     |||||||||    || ||||| ||||   | ||| || |||
TGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCAAgtatgtactgtctgataatcagttttactggcaacccttgtggtttcttttagatgaaaatatttatgtatatggcttcctgatattcttcattcattttacag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 9
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcag
| ||     | ||||  ||||| ||||| |||||||| || || || ||||| || ||||| ||||||||||||||||| ||||| || || || |||||||| ||    |       ||  ||   |||  |     | | |   ||||  | | | ||  ||         ||||||||   ||||| ||  ||||
TATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCAAgtacgtgaaattcttcaacacattcattaggcatgtacaagatagctactaatgatactactta--------actgattttaa-tttccctgccgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcag
| |   | |||||||| ||||| ||||| ||||| ||||| || || ||||| ||||| || |||||||| ||||| || ||||| ||  | || |||||||||||||| |    |  ||| ||| ||     || |||||     |   ||  |   |||| ||||  |   |  |||||| |    | | ||||||
TATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCAAgtatgtcttct----aaacagatttcctc----aagttatgtacactg--tccaagtctatgcatacctaa-acatattttcacccaac-tcttgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaat---tatggttcttacttcttacattatgtatactaattgctgatttt---ctctttccatgttgcag
| | | | |||||||| ||||| ||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || || || ||  | || ||||||||| || |  ||  |   | || ||| ||| ||  |   ||||| |||   |       | |      ||||||    || ||   ||  || | |||| |||
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcct--ctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgc-tgttacag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 9
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaa---ttgctgattttctctttcca-------tgttgcag
| | | | |||||||| ||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| || || || ||  | || ||||||||| || |  || ||     || ||| ||| ||  ||||   |    ||  ||   ||  |  || |||   |  || ||||  | | |  |       |||| |||
TATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcct--ctagac---attcttcaagctaag-ttatatatggatctatttgggttgggggtagtaacactgtctaatttgatttattaaaacttgttgttacag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 8
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcag
| ||     | ||||  ||||| ||||| |||||||| || || || ||||| || ||||| ||||||||||||||||| ||||| || || || |||||||| ||    |       ||  ||    ||  |     | | ||  ||||  | | | ||  || ||| |||  |          |||| || |||||
TATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCAAgtacgtgaaattcttcaacacattcatgagacatgtacaagattgctactaatgatactactta-actgattaat----------ttccctgctgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattcagtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgttgcag
|||   | |||||||| ||||| ||||| ||||| ||||| || || ||||| ||||| || |||||||||||||| || ||||| ||  | || ||||||||||||||  ||  ||  || ||| ||  ||| |  || |     |   ||  |   |||| ||||  |   |  |||||   |     | ||||||
TGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCAAgtatgtctt--ctaaat--agatttcct--caagatatacgcacactg--tccaagtctatgcatacctaa-acatatttttcatccaactcttgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtc---ttttctggattcagtttttctagcaaaaattatggttcttacttcttac-attatgtatactaa---------ttgctgatttt----ctctttccatgt---tgcag
||||  |  | ||||  ||||| ||||| ||||| || || || || ||||| || ||||| |||||||||||||| |||||||| || || || |||||||||||    | | | |||       | |  |     | | ||  |  || | | || | |  ||||  | |||         |||||||| ||     |||| |||  |   |||||
TGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCAAgtatgttaattatccaggaagtgaagtattgaaattcattcatcttcattccattttgccaaaatgttgattaaactgtgatgttgctgatgttacagttcttaccaaatgtttgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 9
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttc-tggattcagtt-------tttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttccatgt-tgcag---------------
| ||  |  ||||||| ||||| || || || |||||||| || |||||||| |||||||| ||||| ||||| ||||| ||||| || || || ||||||||||| ||||| || |  || ||       ||| | |  |  |||    || ||| |||  | | || ||  | || | ||||  |  || |||  || | ||                  
TATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCAAgtatgtattttcctgaaagcaattggaacattttttggtcaggatttatatttttatttcaaaaaataggt-cattactggctgtatgcctgttttaatttctgtctataaaatttccacag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 5'ss of exon 8
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttctggattc--agtttttctagcaaaaattatggttcttacttcttacattatgtatactaattgctgattttctctttcc---atgttgcag--------------------------------------------------------
| ||  || |||||||||| ||  | || ||||| ||||| || |||||||| |||||||||||||||||||| || |||| |||| |    || |||| ||| ||   |||  |  ||  || ||   |     | | ||  |  |  | |    |||| |  ||| ||     |||||      ||||    | |||| ||                                                        
TTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCAGgtacgttccttcatgcctcttagcttcgatgttctatactagcgaacgaa-tggcaacatcaaatattcttgagactgatgcgtaatttcttggaggttggagttatgatactgatgcttgtcatcaacgtgacattaatgcactttggtgattcacag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 9
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttttc-tggat-tcagtttttctag----caaaaattatggttc--ttacttcttacattatgtatactaattgctgattttctctttccatgttgcag---------------------------------------------------------
| ||  || |||||||||||||  | || ||||| || || || |||||||| ||||||||||||||||| || || || | |||| |  | || | |||||| || || |  || |  ||||||| | | |       ||||||   ||   |||  ||  | ||| |    ||  ||     |||| |||    |  |   ||                                                          
TTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCAAgtacgttttataatgtacctcagtttctatgggtgttgcaaattagtatttgtttatgtcgaatatttttggaacagatgtagaatttcctcggaactagacccattattcaatgctgatactaagcgtcaatgttatgttgatacgttttggttaattgcag

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S207_23V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgta------tgtcttttctggattcagtttttctagcaaaaattatggttctta--cttcttacattatgtatactaattgctgattttctctttccatgttgcag
| ||  || ||||||| ||||||||||||||||| ||||| || |||||||| || || || ||||||||||| || ||||| ||  |  | ||||||| |||        ||| ||||| ||     | | ||  ||   | |      | ||   |  ||| |||||    |   |||  | ||  | | | |  |        
TTTTCTACTTGAGTGGGATTCTTACTGTCTTCTTTTGTGGCATTGTAATGTCCCACTATACCTGGCATAATGTTACTGAAAGCTCCCGAATAACCACCAGgtaaacaaccatctcttctgaatcggaatgtcctgtcattcaatggaacacctaagttgtttaaattatagtcatatattaat-atcctttgtcttaacac-----

upper sequence: GRMZM2G063492_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatg----tcttttctggattcagtttttctag-caaaaattatggttcttacttcttacatta--tgtatactaattgct---gattttctctttccatgttgcag
| ||  ||||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| ||  | || || |||||||| |    |||| | |   ||  | | | ||   ||   |  |   || |||  | ||  ||        ||| |   |||   |||||  ||| |           
TTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCAAgtaggcatctcttctttcagttgggatgtccttttcatctaacagaatttttatctgttgaataggccacgtacaagcagctcaagatttagtctatttg--------

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|18963600|gb|BM660526.1|BM660526
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTC
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTC
EST: gi|71311178|gb|DR791899.1|DR791899
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTCTTCCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
EST: gi|89106454|gb|DY576671.1|DY576671
EST:     TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
genomic: TCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
EST: gi|18963602|gb|BM660527.1|BM660527
EST:     GCATAATGTGCCAGAAAGTTCTAGGGTTCCCCCCAA                         GCATACTTTTGCACCTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
genomic: GCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA
EST: gi|67026824|gb|CO455573.1|CO455573
EST:     CACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGGTTAC-ACCAA                         GCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTTCTCTA
genomic: CACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGG-TTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 168

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 298

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 311

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

TGTTGGACCTGAGTGGAATTCTTACTGTCTTCTTCTGTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGTTCTAGGGTTACCACCAAgtatgtcttt ... catgttgcagGCATACTTTTGCAACTTTATCATTCATTGCAGAAATTTTCCTTTTCCTCTATGTTGGGATGGATGCATTGGACATTGAGAAGTGGAAATTAGCTAGTAGC