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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatctatagtccttgattgatgtggaacaaacagttatgtgcatgagaatcttatccctgttctttcaccggaggttaataattcagagttgca...

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 3
TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatctata-gtccttgattg-------atgtggaacaaacagttatgtgcatgagaatcttatccctgttctttcaccggag--gttaataattcagagttgca
|||||||||||||||||| ||||| |||||||| | |||||||||||| |||||||||||||| ||||||||||||||||  ||| ||||  | ||||| |||||| ||| ||| | || | | |        ||||  ||  |  |||||||  ||||||  |   || |   || ||   |  ||   | |  ||||           
TGATCATGCAAACAATCTCGCCTCTAAAATCCGAAGCAACTTGACTAATTCAATGAAAGCTCTGGGAGTGGATATATTGAGTGGTTTTGGTGCAATTGTTgtaagtcatccataagaccataacttcactgtcatgtacaatcatgagttatgcacatgagtgttacattctcatttttgggcaagaacagatgttaata----------

upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 3
TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaa-gttatctatagtccttgattgatgtggaacaaacagttatgtgcatgagaatcttatccctgttctttcaccggaggttaataat--tcagagttgca
||||||||| || || ||||| |||||||||||||  || ||||| |||||||||||||| || ||||| || ||| | || ||| |||| |||||| |||||| ||    ||| |    |||    | |     |   |   |||  || || | |  |||   ||    |          ||    ||  |||   |||  
TGATCATGCTAATAACCTTGCTTCGAAAATCCGTAATAATTTGACCAACTCAATGAAAGCACTTGGAGTAGACATACTTACTGGTTTTGGAACTATTCTGgtaatgtggcatattgcttgtgagaattctatggtat-tataaatgctca-gatattagtattgttgaatgtgtgtgcagttttgtgtatggtcactattgt-

upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 3
TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaa-gttatctatagtccttgattgatgtggaacaa-acagttatgtgcatgagaatcttatccct-gttctttcaccgga--ggttaataattcagagttgca
||||||||| || |||||||| |||||||||||||  |||||||| |||||||||||||| || ||||| || ||| | || ||| |||| |||||| |||||| || |  ||| | |  |||    | |    ||  | |  |   |  ||   | | | ||| || | | | | |  |||  | || | |||  | |      
TGATCATGCTAATAATCTTGCTTCGAAAATCCGTAATAACTTGACCAACTCAATGAAAGCGCTTGGAGTAGACATACTTACTGGTTTTGGAACTATTCTGgtaatgtgacatattgcctgtgaggattctatggcattataaatgcttagatatcagtatgatcactcgctttgtgatgggaatgtttgaaaatagaaaa-----

upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 3
TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatctatagt---ccttga-ttgatgtggaacaaac--------agttatgtg--catgagaatcttatccctgttctttcaccggaggtta-ataattcagagtt-gca-----------------------------------------
|||||||||||| ||||||||||| |||||| | |  |||||||| || ||| |||| | ||| ||||| |||||| |   |||||||||||| ||| |||||  ||   |||| |    ||||| ||  | |     ||          | |||||    |||||||||||   |  |    ||     | || | | |||||||   ||| |||                                         
TGATCATGCAAATAATCTTGCCTCAAAAATCAGAAGTAACTTGACCAATTCATTGAAGGGTCTTGGAGTTGATATACTTGAAGGTGTTGGCACAATTTTGgtacattccatatactatctcttgagttagtttattttaattttgtttttaattatgcattcatgagaatctagccattcaggttattttgaagttaatataattctatgtttgcactggttagaattatgattttactatttatggatttattcag

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|76930812|gb|DV172515.1|DV172515
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGTTTTCC-AGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|211514679|gb|FL210543.1|FL210543
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|74241377|gb|DT649291.1|DT649291
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAA-GGTACGATATGGAAAAGCTGTTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|148935731|gb|EC879774.2|EC879774
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|211514677|gb|FL210541.1|FL210541
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|67016819|gb|CO445568.1|CO445568
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAAGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|149080928|gb|EE170014.2|EE170014
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCC
EST: gi|149105215|gb|EE290703.2|EE290703
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|71305164|gb|DR788719.1|DR788719
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|211514673|gb|FL210537.1|FL210537
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|31354606|gb|CD438963.1|CD438963
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAAGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|211514680|gb|FL210544.1|FL210544
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|149109075|gb|EE189994.2|EE189994
EST:     CA-TGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGC
EST: gi|71444407|gb|DR825457.1|DR825457
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|148974340|gb|EE025114.2|EE025114
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|211517024|gb|FL210545.1|FL210545
EST:     AATGAAAGCTCTAGGAGTGGATATATTGGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: AATGAAAGCTCTAGGAGTGGATATATTG-ACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|148962188|gb|EE013003.2|EE013003
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|148969109|gb|EE019845.2|EE019845
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|149014894|gb|EE044611.2|EE044611
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
EST: gi|149086903|gb|EE176446.2|EE176446
EST:     CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTG                         GGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC
genomic: CAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATC

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: 237

TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatc ... tcctgactagGGAAAGCAAAAGGTACGATATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCATGCAAACAATCTTGCCTCGAAAATCCGTATCAACTTGACTAACTCAATGAAAGCTCTAGGAGTGGATATATTGACAGGTGTTGGCACTATTGTGgtaagttatctatagtccttgattgatgtggaacaaacagttatgtgcatgagaatcttatccctgttctttcaccggaggttaataattcagagttgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA