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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttgctgagttttccatgtacaggtcacctgtgattgtagaacatgttgggaagcactaatcttctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG

Basic information

species Zea mays
transcript GRMZM2G370852_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 4
gtacctt-gctgagttttccatgtacaggtcacctgtgattgtagaacatgttgggaagcactaatcttctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
|||| |    ||| | | | |  | ||||   |  ||| ||  | |       ||  || | ||| || ||||||||| | ||||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||||||||||||||
gtacttccagtgaatgtgcta-atgcaggaatctggtggtttcata-------ggacaggattaacctgctccaattgttgtctagGTTCTCCTTGGTACTGATTCTCATACATGCAATGCTGGAGCCTTTGGCCAATTTGCAACTGGAATTGGAAACACTGATGCTGGTTTTGTGATGGGCACTG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 5
------------------gtaccttgctgagtttt--ccatgtacaggtcacctgt--gattgtagaacatgttgggaagcactaatcttctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
                       ||  |   || |    | |||  | |||  |||  ||  | ||      |   |     ||||| |    |  || |  |  |||||||| | |||||||||||||| || || | ||||||||| ||||| |||||||| || || ||||| || |||||||| || |||||| |||| ||| 
ggttcgcttagtttaaccagtttttattttattatagtgaagtattgttcatttgtttgacagaagtttggttcctgctttgctaatttctctctgttacc-tgcaGGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGCCAATTTGCTACAGGGATTGGTAATACTGATGCTGGCTTTGTGCTGGGAACT-

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 5
------gtaccttgctgagttttccatg--tacag------gtcacctgtgattgtagaacatgttgggaagcactaat-cttctccaattgctatct--agGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
       ||  ||    ||||||   |   || ||       |      |   | |   | | ||| ||   | |   | ||  |     || || ||  |||||||| | |||||||||||||| || || | ||||||||| |||||||||||||| || || ||||| || |||||||| || |||||| |||| ||||
gtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGTAATACTGATGCCGGCTTTGTGCTGGGAACTG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtaccttgctgagttttccatgtacaggtcacctgtgattgta---gaacatgttgggaagcact---aatcttctccaattgctatc-tagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
      | ||   | |  |    |||    | |  | |||||||| |   | |  |||| |       |   |||  | |    || ||||  |||||| |  | || || || || || || || | ||||||||| |||||||||||||| || || ||||||||||||||||||||||||||| | |||||||
gtaaagatctctttca-ctggatatgattggctttcttgtgattgaatatggatttgtttgattatgttcgaaatgatgtgttttttctattatagGTTTTGTTAGGAACAGACTCACACACTTGTACTGCTGGAGCATTTGGTCAATTTGCTACAGGGATTGGAAACACTGATGCAGGTTTTGTGTTAGGCACTG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------gtaccttgctgagttttcca----tgtacaggtcacctgtgattgtagaacatgttgggaagcac---taatctt--ctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
                                                   ||  || | |||  | | ||     ||  |   ||  |    || | | |  | | |  |   |      ||| |  || |||| |   |  |||||||| | || || ||||| || || |||||||||||||| |||||||| |||||||| || || || |||||||||||||| ||| | |||||||| |
gtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgt--agGTTCTCTTCGGCACAGATTCCCACACTTGCAATGCTGGAGCGTTTGGTCAGTTTGCAACAGGGATCGGTAACACTGATGCAGGCTTTATTATGGGCACCG

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|24764746|gb|CA399909.1|CA399909
EST:     GTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAG                         GTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAA
genomic: GTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgct ... tgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtgattgtagaacatgttgggaagcactaatcttctccaattgctatctagGTTCTCCTGGGTACTGATTCTCATACGTGCAATGCTGGAGCCTTTGGTCAATTTGCAACCGGAATTGGAAACACTGATGCAGGTTTTGTGATGGGCACTG
                            cactaat  putative branch site (score: 2)
                               taatctt  TA-rich tract