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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA

Basic information

species Zea mays
transcript GRMZM2G103059_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|||| | || | || ||| | | | |||| || | | | ||| |||| | | | | |||| | || |||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
-----------------------------------------------------aattatgca--catttgattatt-gtttataggcctgc-gatgtccattccacattcagtatt---tgttaagctgagtgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| ||| | | | | | | || | | | |||| | | | ||| ||||| | || ||| | |||| |||| ||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
------------------------------------------------gcttctgattatgcacatttgattgtgttgtttataggcctgctatgtgctttccaataaccagtat------ttgtt---aaatttgtttcatatttcttatgt---atagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgacc--ctccaaataat--aatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatg----ttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || || || | | | |||| ||| ||| | | || ||||| || | || | | || || || | | | | || | | || || | | ||||||||| || || |||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
----gttttaaccattggtttgctgaatgtgtcttcagtgttgaaaa-atttggacacatttgcttcaaattatgcacattcgactgttgtttataggcctgcgatgtccattccacattcagtatttgttaagctgactgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| | || | | | || | | | || | | | | || ||| || | | |||||||| ||| | ||||||||||||| ||||| |||||||| |||||||||| ||| ||||||| ||||||||| |||||||||| || || || |||||||||||||| ||||
----------------------------------------------------------------------gtaacct---catcttcttcaactctcatccgtttgattgcaca---atttctgattt--caattatggtttgttt-----gtt-tgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| || || ||||| | | | |||| || || | | || | | ||| | ||||| | |||| ||| |||| || || ||||||||||||||| || || |||||||| |||||||||| || ||||||| ||||||||| | |||||||| || || || |||||||| ||||||||||
---------------------------------------attaggtttgattgaattggttat-----tggttatttggtca--tggttgct-----atgctggaaaatgt---taaaatgcttttttcttttgt------tgttgtgaataataaatagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACGCTGCACAAGGTTACCCAATACAAGAAGGGTAAGGATAGCA

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || | ||| || ||| || | | | || | | | | ||| ||| || | | |||| || || | | ||||||||||||| ||||| |||||||| |||||||||| ||| ||||||| ||||||||| |||||||||| || || || |||||||||||||| ||||
--------------------------------------------------------------gtaagctcatcttcaatcttcatccctcaactctcatccgtttgattgaaca---actcttgattt--caattatcgttt--tttgtttgct-tgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || | |||| | | | || |||| | | | | | || || | | | || ||||| | || | | ||||||| | | ||||||||||||| || || |||||||| |||||||||| || ||||||| |||||||||| | |||||||| || || || |||||||| || |||||||
-------------------------------------------agtgaattagatttgaaattgcgga--attggttattaggtcgtgtttggtagtacgctgcaaaaatgtta--aaatgcttttcc------ttttgtttgttg-------tgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| || ||| ||| || || ||||| || | | | || ||| | || || | || ||||||| | || |||| | | ||||||||| |||| || || ||||| || |||||||||||||| |||||||||||||| ||| | ||||||||||| ||||||||||| || || ||||||
----------------------------------gttctgaagggcgtatttagattcacttctatgatcgtaattaattctgt-----------atgctgttgaaactgtatcttgtg-gtagttttaa-------acttggttt-------tctgtagGTGAACATTCCGAAAACTAAGAACACTTACTGCAAGAACAAGGAGTGCAAGAAGCATACCTTGCACAAGGTGACGCAGTATAAGAAAGGTAAAGATAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| ||||| | | || | || | || | | | || || |||| | | ||||| | || | || || | | | | | ||| | ||||||||||||| ||||| |||||||||||||| |||| ||| ||||| | |||||||||| | ||||||||||| || || ||||||||||||||||||
------------------------------------ggtgtaaaaagagcct--gttatacttcggttttttagtcttgttatctggct---------ttcttt--------ttcaatatgttttgttga-atatgaaatatatat----tgtctcacagGTGAACGTTCCAAAGACAAAGAAGACGTACTGTAAGAGCAAGGAGTGTAGGAAGCACACCTTGCACAAGGTGACACAATACAAGAAGGGCAAGGATAGCT

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| ||||||| | || | | | | | | || ||| | |||||| | | | ||| | | |||| ||||||| ||||| ||||| |||||||| || || |||| ||| ||||||| ||||||||| | ||||||||||| ||||| |||||||| || ||||||
---------------------------------------------------------atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgt-tttggttaaatgtgga--atatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 3'ss of exon 2
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| |||| | | | ||| | ||| | | | | | | ||| | | | || || |||| || ||||| |||||||||||||| |||||||| | |||||| |||| || |||||| | ||||||||||| ||||| ||||| || || ||||||
------------------------------------------------------------aagtaaagaaatattagacattggcattgttagatttttttttgcaattctttttcgtaattactttgtttgaatatgaatcattctctggctttggcagGTAAATGTTCCAAAGACCAAGAAGACTTACTGCAAAAGCAAAGAATGCAGAAAACACACCTTGCACAAGGTGACACAGTACAAGAAAGGAAAAGATAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S6_198V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| | | | | | | || | ||| ||| ||| || | | || | | ||||||| || ||||||| ||||||||||| |||||| | | |||| || | ||||||||||| ||| | ||||||||||| ||||| |||||||| ||||| |||
------------------------------------------------------gttggttaatggtgcgagatcatgtggatgcgtttagtgtggaggatttgaagaacgat------tgctctattggttttttacttttgtttatggcgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCT

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S115_63V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | || | || |||||| || || || || | | | || || ||| | | | | || |||||| | | ||||||||||||||| ||||| |||||| | | ||| | || | ||||||||||||||| | ||||||||||||||||| |||||||| ||||| |||
----------------------------------------------gaatggcggatg----cgtgagccctagtttatct---tgtct---gagtgattgtgcatgttgaatttgaggtttgg----ggctcgtaacttttgttgatggtatggaatagGTGAACGTTCCGAAGACGAAGAAGTCCTTCTGTCCGGGGAAGGCATGCAAGAAGCACACCCTTCACAAGGTGACTCAGTACAAGAAGGGGAAGGACAGCT

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagact---cttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || || |||| || ||| | | |||| ||| | | || || || | | | | | ||| || ||| | |||||||||||||| || ||||||||| | | ||| || | |||||||||||||||| |||||||||| || ||||| |||||||| ||||||||
----------------------------------------------------tagtaga---tctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtg--actctgatg---gaggcttg---catgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S2_415V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaatt--gaccctccaaataataatttat---------------ccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttata-tagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| ||| | || || | | | || | ||| ||||| || | || || | | | |||| ||| || | || | | |||| || | || | | |||| | || | | | | |||| | | |||||||||||||| || || |||||| | | ||| || |||||||||||||||| |||||||||| |||||||| |||||||| ||||||||
gttagcattccatccattccttctgctccggactcagtgcatttgttagttaggattatttcaaaggtgttacatcttcgatgctgctccttgtgatttggatgggacatgcaatgtcagctgtgtgaatagttgtttttggcaattgttaggttttactgttg-atgatcctcactgaggattgcatgatttgctagGTGAACGTTCCGAAAACGAAGAAGTCCTTCTGTCCTGGGAAGTCGTGCAAGAAGCACACCCTCCACAAGGTCACTCAGTACAAGAAGGGAAAGGATAGTC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ05955 (Selaginella moellendorffii), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttt--taacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | | || | | | | | || | | | | | ||| | |||||||||| || ||||| |||||| | | |||| | || | ||| ||||||||| |||||||||| || ||||| |||||||||||||| |||
-------------------------------------------------------------------------------------------------------gtatgttcttgcgaggcgctcgctgctcagatcttagatctctccccaatgccg-acagGTGAACGTCCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttt--taacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | | || | | | | | || | | | | | ||| | |||||||||| || ||||| |||||| | | |||| | || | ||| ||||||||| |||||||||| || ||||| |||||||||||||| |||
-------------------------------------------------------------------------------------------------------gtatgttcttgcgaggcgctcgctgctcagatcttagatctctccccaatgccg-acagGTGAACGTGCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
                   ttttaac  putative branch site (score: 2)
 aaatgttgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG