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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtggctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG

Basic information

species Zea mays
transcript GRMZM5G862107_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 4
gtattgtg-gctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgtt-----gcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
||||| | || | || |||| | |||| | | || || ||||||| ||| | ||| | || ||| ||||||||||| || ||||||||||||||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||||||
gtattttttgcattcgtacttgagaaaagtatactatctaaagtttatagagctaaggccagagtattttttttaaatgctattagGTTATGATTCTAAGCCATGACCGTGAAAGAGGCCGTGTTAGTCTTTCTACTAAAAAGCTTGAGCCGACACCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G03660.1 (Glycine max), 3'ss of exon 4
--gtattgtggctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgctta--tagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
| | | | | || | || | || | | | || ||| | | | || || ||||| ||||| | || |||||||| || ||||| | || || ||||| || |||||| | || || ||||||||||||||||| |||||||| |||||||
gtaaacctatgataagctatgtgagtatttgcttggaatcacagatgttatgtggaaattaaatctaatttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGAAGGGTAAGTCTTTCCACAAAGAAGTTGGAACCCACACCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G14550.1 (Glycine max), 3'ss of exon 4
--gtattgtggctgtggt-tcttggttgttatgccatatc-catacttaatggagctaacaccaatgaattctgttgctta--tagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
| | ||| | | | || || ||| || | | ||| | | | ||| | | || || ||||| ||||| | || |||||||| || ||||| ||||| || ||||| || |||||| | || || || |||||||||||||| |||||||| |||||||
gtaaacttatgctaagctatgccagtatttgcttggaatcacagatgtcatgtggacataa--aatcttgtttattatttggttagGTGATGATCTTAAGTCATGACCGAGAGAGAGGACGAGTAAGTCTTTCCACAAAGAAGTTGGAACCCACGCCTGGTGACATGATTCGCAATCCAAAGCTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G04190.1 (Glycine max), 3'ss of exon 4
---gtattgtggctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
| | || | ||| |||| | | | ||| | || | | |||| | | ||||| ||||| | ||||||||||| || ||||| ||||| || ||||| ||||||||| | ||||| |||||||| |||||||| |||||||| |||||||
gttaacctatattaatgttatgtggatgtt------tgcctagactcttggacataaaaatctcaagtttcttatttgtttagGTGATGATCTTAAGCCATGACCGAGAGAGAGGTCGAGTAAGTCTTTCCACTAAGAAGTTAGAGCCCACACCTGGAGACATGATTCGCAATCCAAAGCTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G30510.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattgtggctgtg-gttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
|| |||| ||| || | | | | | | | | | || | || || ||||||||||| |||| || |||||||| ||||| |||| || || || || |||||||| ||||||||||||||||| ||||| || || || || ||||
-----------gtatactcttaaacgtt------taatttcagatgttaaaacaacagtccctaacttttaatg--tacagGTTATGATATTGAGTCACGACCGTGACAGAGGAAGAGTAAGTCTCTCCACAAAGAAGCTGGAGCCAACACCTGGTGATATGATTCGTAACCCAAAACTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0077g00450.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtattgtggctgtggttcttggttgttatgccatatccatacttaa-tggagcta-acaccaatgaattctgttgct-----tatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
|| ||| | || | | | | | | | | ||| | | || | || || |||| || | ||||||||||| |||||||| |||||||| |||||||| || || || || ||||||||| | || || || ||||| |||||||| |||||||| |||||||
gtttgcctataatatactgtcaatactgtcaccaaatttcttccactccctacagataaataaatgtatgtatttattttttgtgtttctcttgctgtagGTTATGATCCTGAGCCACGACCGTGAGAGAGGCCGTGTAAGTCTCTCAACTAAGAAGTTAGAACCTACCCCTGGAGACATGATTCGCAATCCAAAGCTTG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S40_14V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------gtattgtg--gctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaa-tgaattctgttgct-----------tatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
|||| | | | || || | | | | | | | | || || || ||||| | || || | |||||||| | |||| || ||| || ||||||||| |||| | || || |||||||||||||||||||||||||||||| | || || || | | |
gtatttagtgttcttcaagactatgcttttctcacagctattcacagaaatgcccgttgagaagtttatacatagtatttctccgatcatattattttatcatacagcatgaaagtggagggttttgtgcagatgacgaggatatcattaactgaataatttttctggctgagttcatccagGTTATGGTCTTGAGTCAGGACAAGGACAGAGGCCGAATCAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGTAACCCACAATTGG

upper sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S32_313V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------------------gtattgtggctgtggttcttggttgttatgccatatccatactta--atggagctaac-accaatgaattctgttgct----tatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
| | | | | |||| | | || | | | | ||| || || | || | ||||| |||| ||||| |||| || || || |||||||| | || | || || |||||||||||||||||||||||||||||| | |||||||| | | |
gtacttagtcttaccagtctttgtagaagtgaatggtgtttagtccgtgcacatggatcttcacgaactatcacgcatgttgacataagttgattgtcttctttccttcgtttataagacttgatgacttcat-atgtgagtggtaaggatgtgtcttaccattaacatgtcttgttgtgattgcgcagGTCATGATTTTGAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGG

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|116813883|gb|EC856377.1|EC856377
EST:     ACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAG                         GTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACT
genomic: ACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACT
EST: gi|32935407|gb|CF040219.1|CF040219
EST:     ACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAG                         GTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACT
genomic: ACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACT

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: 76

TGACATCGGTGGAATCAACGGCCTTCTCCATGTGAGCCAGATTAGTCATGACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 628

TGACATCGGTGGAATCAACGGCCTTCTCCATGTGAGCCAGATTAGTCATGACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

TGACATCGGTGGAATCAACGGCCTTCTCCATGTGAGCCAGATTAGTCATGACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 218

TGACATCGGTGGAATCAACGGCCTTCTCCATGTGAGCCAGATTAGTCATGACCGTGTTGCAGATATCTCAACAGTTCTGCAACCAGGAGATACCCTCAAGgtattgtggc ... ttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG
                        agctaac  putative branch site (score: 218)
 ttctgtt  putative PPT
 atacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtggctgtggttcttggttgttatgccatatccatacttaatggagctaacaccaatgaattctgttgcttatagGTTATGATACTGAGCCATGACCGTGAAAGAGGCCGAGTCAGCCTTTCTACTAAGAAGCTTGAGCCAACACCTGGTGACATGATCCGCAATCCCAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT