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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 4
----tgggtgcattt---tttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatga-ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
    |  |  || ||   |||   |   ||  ||| ||   |  ||||| ||||    | | | | ||||    ||| ||| ||  || ||||   | || | ||||||||||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||
aagattagcacaattgggtttgcagacccaaatgtgttgcctaccatttcttgt----tatacctattgt----tcttacagaagcctgctgggcaacttttgtgcagGGAAAACTGTTTTTACCAGTGATCATGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
 |||  | || || | ||  ||        | |||    | ||||||    | | ||| |||       | |  |||    ||    | | |  || |||| || |||||  |||| ||||| |||||||| ||||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
ggggatctttgttcactgatactgtccctcttgtttttctgttttgttatttcttcttcttggtatcattaatgaaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
   || | ||| || || ||  | ||  | | ||| |       ||   ||||          ||  |  |   ||  | |||    ||    |  ||||| || |||||  | || ||||| |||||  ||||| | ||||| || || || ||||| || ||||| ||||||||||| ||||| ||||||||||||||
---gtacgtttcttgttttgg-acgtagagttgttaagggagcatgcagactt---------gattattccttgaatgtttacattttggcgct--gcagGAAAGACTGTGATCACCAGTGACCATGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
               |   ||   | |  |  | ||  ||  |   |    | |  || |   | ||||   | | | | || | |  || ||||      ||  |    |||||| || |||||  | || |||||||||||| ||||| | ||||| ||||| |||||||| || || || ||||||||||| || || ||||||||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccc-taatattcc-tcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 3
tgggtgcattttttat-tgtgacatgtgtatta-gttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
 |    | ||     |   ||  || |  |||   || || |||     | | | | ||  |         | || || || |    | |  |  | |||||||||||||||| | || |||||||| ||||| ||| | || |   |||| || |||||||| |||||||| ||||| |||||||| |||||||| |||||
-gaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggattactaattttt-tcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 4
tgggtgcattttttat-tgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
      | ||     |   ||  || |  |||   |    ||||   || |  |    | ||   |          |||| |    | |  |  | |||||||||||||||| | || |||||||| ||||| ||| | || |  ||||| || |||||||| |||||||| ||||| |||||||| |||||||| |||||
-aaaaaccttgaaagtgcctgttatcttcattttattcacttttgcatggaaatctgctattccctcaggatgactaattttttcaggtagtggtctgcagGGAAAACTGTAATAACCAGTGATCAAGCACTTAAATTGGAATTTGTTCCCGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattcta----ctggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
    | | | | ||   || |  ||   | |   | | ||   || |||   |   ||| | | |||  ||| | | |||||    |  ||| || |  ||||||||| |||||  |||| || |||||||| || ||||| ||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||
---ttccttgtattccagttatctgcaaaatctataatatgaatt-tgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 4
-tgggtgcattttttat-tgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
  ||    ||| | ||  |||  |   |||  |    || ||   |   | ||| |  |||  ||    |        | || |     || ||||  ||||| || || || ||||| |||||||| ||  ||||  | ||||   ||||||||||||| || || ||||| || ||||||||||| || |||||||||||
taggaaaaattatgtaggtgttgcccatgttctgaacgatatagctgcagcactgtttttgaagtgaacttgatgcttactcaaaaacctggttat--gcagGAAAGACCGTTTTTACAAGTGATCACGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttg-ttgtatgttctcacaaaattctactgga-tgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
   ||  |    | || ||     ||| ||||     | |||   || ||   |  | | |||||         |    |  |    | ||  | ||| |||| || || || || || || |||||||| ||||| || ||||   | ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||
---gta-agaagtcatggtcgttggtggattaaaatgcttttaaagtttatgctggtcgattgtaaaaatgattatctcttgatcaaactgcgtgtatccagGAAAGACGGTGTTCACCAGCGATCATGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGA

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 4
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactgg-atg-attatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
 |   | |  | | || ||        |  || || | ||  |||     |||   |||  |    |    |||||||   | |   ||| |  ||   |||| || || || || || ||||| |||||  |||| || ||||   |||| ||||||||  ||||||| ||||||||||||||||| ||||||||||||||
-gtaagaaactatcatcgt--------tgatactttagatgctttcaaatcttgtattgccgcg-ataagaacaaaatctgattcatatggaggatgctcagGAAAGACGGTGTTCACGAGTGACCATGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGA

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|211514676|gb|FL210540.1|FL210540
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCGGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|211514679|gb|FL210543.1|FL210543
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTC-GNTTCCC
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAG-TTCC-
EST: gi|148935731|gb|EC879774.2|EC879774
EST:     AATCGCCACTGGGTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTA
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTA
EST: gi|211514677|gb|FL210541.1|FL210541
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTC
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTC
EST: gi|67016819|gb|CO445568.1|CO445568
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|6536537|gb|AW224850.1|AW224850
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCGGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|211514673|gb|FL210537.1|FL210537
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCGGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|31354606|gb|CD438963.1|CD438963
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|211514680|gb|FL210544.1|FL210544
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCGGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|148974340|gb|EE025114.2|EE025114
EST:     ATCGCCACTGGTTCAGTTCCTTTTTGT-CCGAAAAGGATTGAGATTGATG                         GGAAAACTGTATTTACT
genomic: ATCGCCACTGGTTCAGTTCCTTTT-GTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACT
EST: gi|211517024|gb|FL210545.1|FL210545
EST:     AATTGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCGGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|148962188|gb|EE013003.2|EE013003
EST:     AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACCTGAA-CTTGAGTCAGTTCCA
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCAC-TGAAACTTGAGTCAGTTCCA
EST: gi|148969109|gb|EE019845.2|EE019845
EST:     AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTT
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTT
EST: gi|149014894|gb|EE044611.2|EE044611
EST:     AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG
EST: gi|149086903|gb|EE176446.2|EE176446
EST:     AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATG                         GGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTTCAG
genomic: AATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAG

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), 45 (downstream exon)
Score: 127

TATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

TATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA


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

TATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 209

TATGGAAAAGCTGGTTTCCCAGATAAAGAAATCACTGCCAGGAACATCATAATCGCCACTGGTTCAGTTCCTTTTGTTCCGAAAGGGATTGAGATTGATGgtaaatgctt ... ttatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA
                     ttctcac  putative branch site (score: 209)
                                         atgattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggtgcattttttattgtgacatgtgtattagttgacattttttgtgtactttccttgttgtatgttctcacaaaattctactggatgattatatgcagGGAAAACTGTATTTACTAGTGATCATGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG