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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaaggaacaggagagcggaactggatggtatatccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 5
gtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaaggaacaggagagcggaactggatggtatatccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA
                   |    ||||  ||   |||    | ||||     ||| | |||      |  |||||||  ||| ||| |   ||| |  |||         |||||     |||||||| ||| |   |    ||||||||||||| ||   || ||| | |||||||| ||||||||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| |||||| | ||||| |||||||| |||
------------------gtagattgcatgccactgag----tttttggctttaagccaatt-----ctttcttgttttatttcaaaggactcagaaatgcgag-------ggtatg---gtttcatcttttgttagtcaactctaattagtttgttttcc-ttctgt-atagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCACATCAGAACATCTAGTGACACTCCTTGCAGTTGTTCCTAAGTACTCTCAA

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 3'ss of exon 5
gtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaag-gaacaggagagcggaactggatggtatatccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA
                                                                         |||  || |||   |  |||||    | |   |||   |  ||||   | |  || | ||   |  || || | |    |||| || || |        |||||||| || ||||||||||||||  |||||||||| |||||||| || || || ||| || |    || ||||||||||| ||||||||||| || || 
------------------------------------------------------------------------gtgtgaatgttatttattgaaca----atcatgactttttaatataataagt--atttcttagctgactttaatgacctatttgcctgtttt--------agCTTAGCTGTCCGTGATCTTTCCAACTTGGTAAAACCTGAGGATATTATAACTTCAGAAAATTTAACCACCCTTCTTGCAATTGTTCCCAAGTATTCACAG

upper sequence: GRMZM2G144372_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattgcattgtcatacttttgtgcagaccctggaggaactgtttgatgccaagaccattacgttttcccttgtttattttaaaaaggaacaggagagcggaactggatggtatatccatttcatctgttgct-ttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA
                                                                          || ||  ||     | ||   |   |  | ||      |       |||| || |  ||   || || | || ||       |||||  |||  | |  || |||| ||||||||||||||||| || ||||| || ||||| || ||  |||| |||||| | ||||||||||||||||| ||||||||||| || || 
--------------------------------------------------------------------------gtataccttggtt-gaaatctgtttgtaggacaaacaag-------attttatttactgtgatttcttttctgatcgacc--tctttgcttgcttca--gCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGCCTCAGAACATTTAGTGACACTTCTTGCAATTGTTCCCAAGTATTCTCAG

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|71428528|gb|DR809578.1|DR809578
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|61117886|gb|DN558847.1|DN558847
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|31558493|gb|CD527705.1|CD527705
EST:     GAAAGCAAAG-GGGAG                         CTTAGCGGTTCG-GATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: GAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|33104344|gb|CF064304.1|CF064304
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|21987710|gb|BQ779238.1|BQ779238
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
EST: gi|67022208|gb|CO450957.1|CO450957
EST:     AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC
genomic: AATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCAC

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: 401

GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 408

GTGCGAGCAGCGGAATATAATAATGTAAGGAGCCAGCTTAGTGCAATCAACAGAAAGCAAAGTGGGAGgtaaattgca ... tgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttcatctgttgctttcctgtactaattagtttgtcttttattgtgtgaaagCTTAGCGGTTCGTGATCTTTCCAATCTGGTAAAACCGGAGGATATGATCACCTCGGAACATCTTGTGACACTTCTTGCAATCGTTCCCAAGTACTCCCAA
                       tactaat  putative branch site (score: 408)
                                     tcttttatt  putative PPT
                          taattagttt  TA-rich tract