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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 13
gtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtata-aaacgaaattcactttcattt-cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG
                  | ||  | ||  |  |  |  || || |  |  |  |  ||||  || |      |   | |  ||| ||| ||    ||||||| |||| ||||| |||||||||| |||   || || |||||||||| |||||||||||||||  || || |||||||||| |||
-----------------gtttggttccttttttttttttccaaaatacaaactct-ttatgtcagtttgatcagttctttgcaaatgaactttgtattcattttcctagtacagATCAGAGAGGATCCTGTCTTCCGTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG
















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|148947432|gb|EC892855.2|EC892855
EST:     GTGCAGATGTTGCCCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     CCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: CCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     GTGCAGATGTTGACCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|32847340|gb|CD987021.1|CD987021
EST:     GTGCAGATGTTGGCCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     GTGCAGATGTTGACCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     GTGCAGATGTTGACCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT

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), 46 (downstream exon)
Score: 438

GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 393

GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 390

GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG
                                ttcactttcatttcct  CT-rich tract
                    tataaaacgaaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA