Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT

Basic information

species Zea mays
transcript GRMZM2G032562_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36830.1 (Oryza sativa), 3'ss of exon 1
------aggcagaattggtgtttgtattg-gccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| | | || || | ||| | | ||| ||| | | | | | || | || | |||| ||| ||| |||| | || || ||||||||| ||||||| | ||||| || |||||||| |||||||||||| |||| || |||||||||||||||||||| ||||||||||| ||| |||| |
tgctggatgattgtctcatgcttctgttgtatccatgtatattgttttttatcattcatgtacaaagtcg-attagattca---tgtgcatgtt--tgtgttt-cagGCTGCAAACTACCTCAACATCAAGGGACTGCTGGATCTGACCTGCCAGACCGTGGCTGACATGATCAAGGGGAAGACACCAGAGGAGATCCGCAAGACCT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G08440.1 (Glycine max), 3'ss of exon 1
aggcagaattggtgtttgtattggccattatattttga-gtgtcaagaaataaatatatt--gtaggattatattgtgactgtccatgctactgca---------ttcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
||||||||||| | ||| | | || || | | |||| ||||| | | ||| | ||| || || || ||||||| ||||| || | ||||| | ||||||||||| || || || | || || ||||||||||||||||||||||||||||| || ||| |||| |
-----------atgtttgtattgtttgt-gcattgcaatgccacataaactctgtttatttagtaggttaagtctgtactaatacatattaatgtgacaattttctttttagGCTGCTAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGTCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCAGAGGAAATTCGCAAGACCT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G05120.1 (Glycine max), 3'ss of exon 1
--aggcagaattggtgtttgtattggccattat--attttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| | ||||||| | ||| ||| | | | | ||| | | | ||| |||| | | | | || || ||||||| | ||| || | ||||| | || ||||||| || |||||| | || || |||||||||||||| |||||||| ||||| || ||| ||||||
gcctgtgtgtgcaatatttgtatgttttaatatcaggtttactctttattatgtcaattaacactggcattcctttgt--tttatgaaaattttctatcca--gGCTGCAAATTACTTGAATATCAAGAGCCTTTTGGACCTTACTTGCCAGACAGTAGCAGACATGATCAAGGGAAAGACTCCTGAGGAAATTCGCAAGACAT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G23230.1 (Glycine max), 3'ss of exon 1
------aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| ||| || ||| || | | ||||||| | | | | | | | || | | | ||| ||| | | | | | |||||||||| ||||| || | ||||| | || ||||||| || |||||| | || || |||||||||||||| |||||||| ||||| || ||| ||||||
taaccattgtagacttt-tgtctgcctgtgtttgcatatttttaatcttagg---tttactctttattatgtca-attaacactcttt-caaaatttcctatacagGCTGCAAACTACTTGAACATCAAGAGCCTTTTGGACCTTACTTGCCAGACAGTAGCAGACATGATCAAGGGAAAGACTCCTGAGGAAATTCGCAAGACAT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G36850.2 (Glycine max), 3'ss of exon 1
aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaata-tattgtaggattatattg-tgactgtccatgctactgcattcac---agGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
|| |||| || | | ||| || || | | ||| || || || | || | || ||| ||| || ||| ||||||| ||||| || | ||||| | ||||||||||| || ||||| | || || ||||||||||||||||||||||| ||||| || ||| |||| |
---catggttgga--ttatctgggcaatggaatgccacatatactctgttaattagtaggttaaatctgtactaatgcatgttaatgtgacaattttccttttagGCTGCGAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGCCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCCGAGGAAATTCGCAAGACCT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
--------------------aggcagaattggtgtttgtattggccattatattttgagtgtca--agaaataaatatattgtaggattatattgtg-actgtccatgc-tactgcattcac-------agGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
||| | | | || |||| ||| | || | || ||| | || || | | ||||| | | || |||| ||||||| |||||||| | ||||| || ||||||||||||||||||||| | || || | ||||| |||||||| || ||||||||||| ||| |||| |
gtaagcgcgcgagaaatttggagcacctcgttcgctcgcat-ggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgcgcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S9_292V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------aggcagaattggtgtt-tgtattggccattatattttgagtgtca-agaaataaatatattgtaggattatattgtgactgt-ccatgctactgcattc-----acagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
||| ||| | | || | || | | | | | | | || | | ||| | ||||| | | | || || |||||| || ||||| || | ||||| ||||||||| |||| |||||| | || ||||||||||| ||||||||||| || |||||||| | | || |
gtaagtgatgtgcatgcgaccctgtttgttgcgtgcagggcgggggatggggtgcatcccagcgggggcggaagcgcgatgatggcgcgtgcaacgtttgtggggcgagagaggagggggtgacttggggtgaggagttgtgctgacgtcggggtggtgaatgatgggaacagGCAGCGAACTACTTGAACATCAAGAACCTGCTGGACTTGACGTGCCAGACGGTGGCGGACATGATAAAGGGGAAGACGCCGGAGGAGATCAGGAAAACGT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S7_342V6.1 (Physcomitrella patens), 3'ss of exon 2
--aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| | | || ||| || | | || | || | ||| ||| | || || | | | || | | |||||| || | ||| || | ||||| || | || ||||| |||||| |||| ||||||||||||||||| ||||| || |||||||| || ||||||
tttagagcacgtcatggctgtcttt-tcttaatgccct-agcgcttttgaatttgtatccttgctacctaaatgaggcttaatgtttcttatttgtgaacagGCGGCCAATTACTTGAACATCAAGAATTTGTTAGATCTGACTTGCCAGACCGTAGCGGACATGATCAAGGGTAAGACCCCTGAGGAGATCCGTAAGACAT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ22022 (Selaginella moellendorffii), 3'ss of exon 1
------------aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaatatattgtagg-attatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| || || | || | | ||| || | | | | | | | | ||| | || | | | ||||| || |||| || | ||| ||||||| ||||| ||||| |||| ||||||||||||||||| ||||| || |||||||| ||| |||| |
gtaggatttcttcgttcgatttcttcccccctttttctctcgcttttctcgttttgggtcttgagctttcgactgacaatcgatttgggtgatctggttttgcgttgttccagGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

upper sequence: GRMZM2G032562_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18284 (Selaginella moellendorffii), 3'ss of exon 1
aggcagaattggt--gtttg---tattggccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
| || ||| | ||| | | || || | | | | | | | | ||| | | | | | | | ||| ||||| || |||| || | ||| ||||||| ||||| ||||| |||| ||||||||||||||||| ||||| || |||||||| ||| |||| |
--gtaggatttcttcgttcgatttcttcccccctttttctctcgcttttctcgttttgggtcttgagctttcgactgacaatcgatttgggtgatttgttc-cagGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

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|211531971|gb|FL228670.1|FL228670
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTAGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|211531964|gb|FL228663.1|FL228663
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTAC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTAC
EST: gi|211528968|gb|FL228657.1|FL228657
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|211540989|gb|FL228708.1|FL228708
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTA
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTA
EST: gi|211359203|gb|FL433599.1|FL433599
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTMCCTGGAGATCAATGGGCTGCTAGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|211540986|gb|FL228705.1|FL228705
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATTCAATGGGCTGCTGGACCTGACCTGCCAGG
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGAT-CAATGGGCTGCTGGACCTGACCTGCCAGG
EST: gi|211537976|gb|FL228694.1|FL228694
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTAGACCTGAACCTGCCAGGC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGA-CCTGCCAGGC
EST: gi|211230724|gb|FL437687.1|FL437687
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|211528961|gb|FL228650.1|FL228650
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|51871192|gb|CV126076.1|CV126076
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|84980315|gb|DW530664.1|DW530664
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|84980304|gb|DW530653.1|DW530653
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCC
EST: gi|211531963|gb|FL228662.1|FL228662
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGA
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGA
EST: gi|211540994|gb|FL228713.1|FL228713
EST:     ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAG                         GCTGCAGACTACCTGGAGATCAATGGGCTGCT
genomic: ATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 24

GCCAAGTGCTGCGAGTAACAAGGCCTCAGCGGACGATCTCAAGTCCTTTGATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 26

GCCAAGTGCTGCGAGTAACAAGGCCTCAGCGGACGATCTCAAGTCCTTTGATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 208

GCCAAGTGCTGCGAGTAACAAGGCCTCAGCGGACGATCTCAAGTCCTTTGATGCTGAGTTCGTCGATGTTGACCTGGTCACCCTCTTGGAGCTCATTAAGgtgaggccct ... gcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT
     aaatatattgtaggat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcagaattggtgtttgtattggccattatattttgagtgtcaagaaataaatatattgtaggattatattgtgactgtccatgctactgcattcacagGCTGCAGACTACCTGGAGATCAATGGGCTGCTGGACCTGACCTGCCAGGCCGTCGCGGACATGATCAAGGGGAAGACTCCAGAGGAGATACGCGAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccatgc