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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG

Basic information

species Zea mays
transcript GRMZM2G027851_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 7
gtgagtcaaact--aggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
|| ||| || |   |  |||| || | |||| |||| | |||| | |             ||| ||||||||| || | |     |||||| ||||||||| ||||||||||||||||| ||||||||||||||||||||||| || || |||||||| |||
gttagttaagcccaaacaaaccctcattagttaacggttttatgctc-------------agtgttaacttggatgttggtga--ctgattccagGCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAG

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 8
-------gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaa--cttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
        ||| |  |      ||| | | ||  |   | || |||||  |     |  | || |  ||  ||  ||   |    | ||  | | ||| |||||| || || || || |||||||| ||||||||| | ||||| ||||||||||||||||| || || 
attataaatgacttcataccacaaataataacctgatgaaga-gttatcaataaaaaagaaattatttaccaaggctgaacaaaattct-ccttaattccagGCACTCTACAGATCGCGAGGTTGCTCTTATGATGTTAATGGCATACCTCTCCTACATGCTTGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 7
-----gtgagtcaaa-ctaggaaaca---cttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
     ||  ||   | || |   |||    ||   |  | || |||  | | | || | ||  ||    ||     |   |   |||||   || ||| |||||| || || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| || 
tctctgtatgttttatcttgatcacaggttttttaaacctaccatgaaa-ataatttgtgataattttttagctgttcaacaaattgct-cactcattgcagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 7
gtgagtcaaactaggaaacacttactagtcaacgatgttata---cacttcgagaacatcaag-tattaacttggctgcttg-----ctgtcc--tgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
   | |  |    |||| |||||| ||      |   |  ||    ||    | || ||   | || |   || | || |        ||  |  | ||| |||||| || || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| || 
--cacttcagt--ggaatcacttattaactggggtcttcgtaatctaccataaaaaaattgtgataattttttagatgttcaacaaattgctcactcattgcagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 8
gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcga----gaacatcaagtattaacttggctgcttgctgtcct----gatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
   ||      ||| |  | |||  | ||    ||  |   |||    ||     ||||     | |||    |||         | ||     ||| |||||| || || || ||||||||||| ||||||||| | ||||| ||||| ||||||||||| || || 
acaaggttttttag-acccgctttttggtatgagacttggcacaggatgatttgaaacaatcttttttactgaggccaaacaaaattctccttaattccagGCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctg--cttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
      || | |      ||  ||   || |    | || |  |  | |    |     |   |||| | | ||  ||  |  |  |  |  |||||| || |||||||| |||||||| ||||||||||| ||||| || || || || ||||| || |||
---gtacatatttaacgtcatatat--gtgacttgttttctttaagttgtttcctgtttggtctaacgtagatggcctcacattaattgtcacagGCACTCAACTGACCGAGAGGTTGCCCTTATGATGCTTATGGCGTATCTTTCTTATATGCTTGCTGAG

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 7
--------------gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
                   |||     | | |||  || || |  ||||   ||  ||     |  |||  || ||   ||||      || ||| |   | | |||||| || ||||| || |||||||| ||||||||||| ||||| ||||| |||||||| || || || 
tttatgataaaacctcagatcatgtaggaatacatataataat--acgagaataatcatactaaagaca--aaatac--acttacagaatttctgaca-aaatccagGCACTCTACTGATCGGGAGGTTGCCCTTATGATGCTTATGGCATACCTTTCCTACATACTTGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtgagtcaaactaggaaacacttactagtcaacgatg-ttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
                 ||  || ||| |||    ||  |    || | |  ||||   || ||| |      | |||  | |   | |||  |   |  | | ||||||||| ||||| || ||||||||  | ||||| |||||||||||||| || || |||||||| || 
attcttttatatcacttgtataagtagtaaatgtctaagaaaagacaagggctata-gttttgagga------gaattctcatactttctttgttaacaaactccagGCATTCGACTGATCGGGAGGTTGCAATCATGATACTCATGGCTTACCTTTCGTATATGCTGGCTGAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 7
----------gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgt-cctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
               ||||   |  |||    |    ||||  || | | |    |||     |    |   |||   |  ||    | ||| | | |||||||||| || ||||| ||||| ||||| ||||||||  ||||||||||||| || |||||  |||| || 
ggtcatattttcatatcaaggcaataaattgatgg-ggtcatagaaggtgttttattcatcttcgcagaactttag--taactaaa-gttgtgcttaatttcagGCACTCTACTGATCGTGAAGTTGCACTTATGATTGTCATGGCTTACCTTTCATACATTATGGCTGAA

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|71437105|gb|DR818155.1|DR818155
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|71761590|gb|DR959527.1|DR959527
EST:     ACTGGATTGCTCAGTGCCTACATAATTAGGAAGCTATATATAGGAAG                         GCATCCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|71758416|gb|DR956353.1|DR956353
EST:     CTACATAATTAAGAAGCTATATATAGAAAG                         ACATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: CTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|78074782|gb|DV503216.1|DV503216
EST:     CAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: CAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|211100374|gb|FL186479.1|FL186479
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|89755589|gb|DY685958.1|DY685958
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|74239374|gb|DT647288.1|DT647288
EST:     CAGTGCCTACATAATTAAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: CAGTGCCTACATAATT-AAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
EST: gi|33100450|gb|CF060410.1|CF060410
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGA
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGA
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAG                         GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC
genomic: ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTC

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), 48 (downstream exon)
Score: 34

ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 26

ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 7

ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 22

ACTGGATTGCTCAGTGCCTACATAATTAAGAAGCTATATATAGGAAGgtgagtcaaa ... ctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG
                                        ctgtcct  CT-rich tract
                   aagtattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcaaactaggaaacacttactagtcaacgatgttatacacttcgagaacatcaagtattaacttggctgcttgctgtcctgatttcagGCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG