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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaagacagtagtcaatattcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG

Basic information

species Zea mays
transcript GRMZM2G034622_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g06690.3 (Oryza sativa), 3'ss of exon 21
gtaaaaagaca-gtagtcaatattcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
|||| |  |    | |||| | | | | || |   || | ||  ||  | |   |     || |  |   || |||||  ||||||| || ||||| ||||| || |||||||| ||||| || || ||||| || || |||||| | |||||||||||||||||| | |||
gtaatacaatgcattgtcatt-tgcttgtcttgaaatacgtt--gatacataatttgccattgtttt---ttttatca-cagATCCGCGCCCAAAGCACACATTTTTTGAGAGGCTTTCAACAACTAATACCGAATGAATGGATTAACATGTTCAATGAACATGAATTCCAG

upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G03680.1 (Glycine max), 3'ss of exon 8
-------------------gtaaaaagacagtagtcaatatt-catatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                    ||||        | |    ||| ||| |||  |      ||   | ||||   | |   |     |  ||  | | | ||||| |||  ||||||| || | |||||||||||  ||||||| ||||| |  || ||||||||||||||||  ||||| |||||| |||||
aaatttacccaagcagggcttaaatttgtttcaatttgaattgcatctcacggtgactgtttttatgcttccattatactaaatataattattgt-attagATACGTCAACAAAGTTCAAATTTCTTGAGAGGACTTCAGCAACTTATTCAGAAGGATTGGATTGATATGTGTAATGAGCATGAACTTCAG

upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 20
------------------gtaaaaagacagtagtcaatattcatatc--attggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                   | |   |||| | |    | | || ||   | |  |  |||        |    |||   |  |  |  ||  | |    |||| ||   ||||||| |||| |||||||| || |||||||| ||||| |  || ||||||||||| ||||| |||||||||||| |||||
tatatactctatctctatctgatgtgacacttgggtttttccaaatgcaaatcaactcatgtttcaattacaataataataataataatta-tgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATTCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 20
-------------------gtaaaaagacagtagtcaatattcatatcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                    ||   | |  |         ||  |  || || |         | | ||   | |  |  |       || | |    |||| ||   ||||||| |||| |||||||| || |||||||| ||||| |  || ||||||||||| ||||| |||||||||||| |||||
ctctattatggctctatctctagccaaagtgacacttgggttttttccaatgcaaatcaacccatgtttcaattacagaataaaataattatgttttcagATACGCCAACAAAGTTCACATTTCTTGAGGGGATTTCAGCAACTTATGCAGAAGGATTGGATTGACATGTTTAATGAACATGAACTTCAG

upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G17205.2 (Arabidopsis thaliana), 3'ss of exon 20
gtaaaaagacagtagtcaatattcat--atcattggatgcattaggaggctttgctaaatgtt--ttcctggtttc----tatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
|||    |  |  | | |    ||||  ||| | | || | | |||   |  ||  ||        |  || | ||     ||    |||| ||    || ||| | || |||||||| || |||||||| || || || ||||| ||||| || |||||||||||||||||  |||||
gtactggggaaccacttacctctcatttatcttggcatacctgaggtcaccctgtaaatcaacagctattgatatcatctcatttgcagATACGCCAGCAGAGTTCTCATTTCTTGAGGGGGTTTCAGCAACTCATTCCGAAAGAATGGATCGACATGTTCAATGAACATGAGCTTCAG

upper sequence: GRMZM2G034622_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 21
gtaaaaagacagtagtcaatattcatatcattggatgcattaggaggct-ttgctaaatgttt-tcctggtttctatcaat---agATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
|| | |   |  |  |||   || ||  | |   |  | |       || |||||  | | |  |      |   |||| |   |||| |||   |||||||| || |||||||| ||||||||||| ||||||| || |||||||||||| |||||  |||| |||||| |||||
gtgagatcgcctttttcatagttaattccttcaaactcttccttgaactgttgcttgacgctaatatcaaataacatcactttcagATACGTCAGCAAAGTACTCATTTCTTGAGGGGTTTTCAGCAACTTATACAAAGAGATTGGATTGAAATGTTTGATGAGCATGAACTTCAG

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|32835669|gb|CD975347.1|CD975347
EST:     ATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGT
genomic: ATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGT
EST: gi|32916888|gb|CF021700.1|CF021700
EST:     TACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAG                         ATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCA
genomic: TACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 51

TGAAGAAGAACTTCTCCCTGGTGGGAGGCACATGCGTGTAACAAATGATAATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

TGAAGAAGAACTTCTCCCTGGTGGGAGGCACATGCGTGTAACAAATGATAATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

TGAAGAAGAACTTCTCCCTGGTGGGAGGCACATGCGTGTAACAAATGATAATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TGAAGAAGAACTTCTCCCTGGTGGGAGGCACATGCGTGTAACAAATGATAATGTTATTACTTTTATCCATCTTGTCGCCAATCATCGGTTAAACTACCAGgtaaaaagac ... ctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattggatgcattaggaggctttgctaaatgttttcctggtttctatcaatagATCCGTGCACAAAGTACACACTTCTTGAGAGGTTTTCAGCAGCTTATACCAAAAGATTGGATTGATATGTTCAATGAACATGAAATTCAG
                        tgctaaa  putative branch site (score: 99)
                                 ttttcctggtttct  putative PPT
                           taaatgtttt  TA-rich tract