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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC

Basic information

species Zea mays
transcript GRMZM2G091490_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
                         |  ||  |  |  ||||  ||     |||   |   ||  |  |||  ||||   || || ||  |  ||||  |   | |  ||  ||   |||||| | |||| |  | |||||      ||| || || ||||||||||||||||||||||||||||||| ||||||||||||||||||| | || ||||| ||      
------------------------gtacgta-attaagcacacacacatcgatcaattcgatcgatttttg-acatgttttg-atcaatgtggcatg-tgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTC------AGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
                                                 | ||  | | | |  |   | ||  |   |||  ||||    | ||||      |   || | |    |||||| | ||||    | ||        ||| ||| || ||||| |||||||| |||||||||||| ||| ||||||||| ||||| |  ||||| ||||||||      
------------------------------------------------gtgatgatttttttgctaagtagctaagataattaatgagtagtgcatgt-----aattgattaatttgtgcagAGATGTGCAAAATAGGA-----AGCAG-CCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
            | ||||   |  || ||  | |  |   |||||||||    | |  ||| |    ||   |||  || |    |    ||   |        |   | |      |||||| || |||    | ||  |  |       || ||||| || |||||||||||||||||||| |||| ||||||||| || || ||||||||||| |||||      
------------gaatattcaaatat-tgcat-catgggtcatgcatga----catgaatcacggcactaatgcac-cattttgaggggtttcttttttcttttctttatt---ttttgcagAGAAATGCAAAATAGGAACCAC------TCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatga-tcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
                    | | || |    |     ||    ||||| ||||  |  ||  |||   |  ||    || |    |    || | |        |     |      |||||| || |||    | ||  |  |       || ||||| || |||||||||||||||||||| |||| ||||||||| || || ||||||||||| |||||      
-------------------ttggaatattcaaatattgcat---catgagtcatgctgcatgacatgaatcacggcatcattttgaggggttt-cttttttctttctatctttctttttgcagAGAAATGCAAAATAGGAACCAC------TCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
                                              |||| ||  | | | |  |   | ||  |   |||  ||||    | ||||      |    | | |    |||||| | ||||    | ||        ||| ||| || ||||| |||||||| |||||||||||||||| ||||||||| ||||| |  ||||||||||||||      
---------------------------------------------gtgatgat--tttttttgctcagtagctaagataattgatgagtagtgcatgt-----aattaattaatttgtgcagAGATGTGCAAAATAGGA-----AGCAG-CCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacaca-tgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
                    ||    ||   || || | | |   | |     ||  | | |||  |  ||     | |  |   |   |   |  | |  | |  |  |        ||||||  | ||  |  |||| ||  || ||      || ||||||||||||||||||||||||||||||| |||||| || || |||||  | || ||||| ||      
------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatg--caaa--------tgcagAGGAATGTAGAATCGGTTCAACGCCA------CAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0048g02660.t01 (Vitis vinifera), 3'ss of exon 1
-gtatgcatccatgcatatagtaggatctgt-gtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgaccc------ctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
  | ||| | |||   ||    |    || |  | |    | | |   |   ||     | |   ||         |   |  |  |        | | | || |  |  |  | |         |||||| |||||  |  | || ||  |      |||||| ||||| ||||||||||||||||||||||||| ||| || || ||||| ||  | || || |||||      
gttgtgc-ttcatatttagttcatcgcctctcattcttttctcttaattttgcaattcttgttgaatattccatcaagatagcgtgtatcttcccctttgtgatgttcatatcggcttgggtttttgcagAGAAGTGTAGAATAGGATCCAC------CCCTCAAAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCAACGGGAACCAGGACTAATCGCGCCACTGC

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------gtatgcatccatgcat-atagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacg--accggactgacccctgcagACAAGTGCCGCGTCGGGT-CG--TCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC
                                                                |||| ||  |||   ||   ||  | |    |    || ||||  ||        |  |   |||||      || | |||      || |||| ||  | |  |||    ||    |  ||||   |||| |  | |||  ||   |  |||    ||| |||||||||||||||||||||||||| ||||  ||||||||  |||| |  ||  | |||||   
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatg-gtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgat-catcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGT-CGTCGTCA--GGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC-------
| ||| |      ||| |   ||||  | | |  |   |  ||   |    ||| |  | | |  ||         || |   | ||| ||| |        | |      || |     |||     ||| |  |||||  ||||  ||  |     ||||  |||||||||||||||||||||||||| | ||| || ||    ||||  ||  | || || ||       
gcatgaacatgctcatttga-aggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatatt-caatttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------gtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgc-aatgcatgaaacttacatggcgacgaccggact---gacccctgcagACAAGTGCCGCGTCGG-GTCGTCGT--CAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC
                                                 ||  | |  |  | |     |    |  | | |  | | | ||  || ||     | ||| |   |   |    |||  ||| |   ||      ||  |  |  | | |||   | |  |  ||||   |||| |  | || | || ||   | |    ||||| ||||||||||||||||||||||||||||| ||| || || || || |  ||| | |||||   
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagat-atggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------gtatgcatccatgcatatagtag-----gatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgc--gcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGT-CGTCGT--CAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC
                                                                    ||  |||  |      || ||      ||  ||||  | | | |    || || ||| ||    |||||   |||   ||||| ||||    |    ||  || | |  ||  |  ||  ||   ||||   |||| |  |||||  || ||   |||  | ||| |  |||||||||||||||||||||||||| | |||||| || || || |  ||  |||||||   
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcat-gttctcctcatctattgatagcatgaaatggtccagcagtat-tgacaaaaacttg-ttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgcatccatgcatatagtaggatctgtgtacg-agacacatgcatgatcatcgtctatct-cattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGT--CGGGTCGTCGTCAGGCCC-TCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC
                   | | ||||     ||  |    |   | |||    |||  || | |||||    |  | | |  | ||    | |   ||   ||     |   | ||  ||||||    |||    |  | ||    | |   |     |||||| ||||||||||||| ||||| ||||||| ||||||||| || || |  ||| |||||||   
-------------------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcat---tgctaactgatag--cgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
gtatg-catccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACA-AGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
||| | |   ||| | |  ||     |||   | ||  | | |   |  | | |  ||| |   | |  |||||     ||||  |    ||  ||  || |     | | ||       || ||| ||  | | | ||  | | |  |  |    ||| |||| |||||||||||||||||||| |||| ||| |||||||| |||||| | |||||| | ||      
gtaagacggtcatccctcaagct---tctcatttcggaaaaaa---aaaaccgt--tctttggaagtctttgcgttctaaatgtctctt-ctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAG-CAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
gtatg-catccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACA-AGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
||| | |   ||| | |  ||     |||   | || || | |   |  | | |  ||| |   | |  |||||     ||||  |    ||  ||  || |     | | ||       || ||| ||  | | | ||  | | |  |  |    ||| |||| |||||||||||||||||||| |||| ||| |||||||| |||||| | |||||| | ||      
gtaagacggtcatccctcaagct---tctcatttcgggaaaaa--aaaaaccgt--tctttggaagtctttgcgttctaaatgtctctt-ctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAG-CAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

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 2 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 35 (downstream exon)
Score: 3

CTGACCTACTACCTGAAGAAGAAGGTGGCGTCGGAGCGCATCGACCTGGACGTCATCCGCGACGTGGACCTCAACAAGCTGGAGCCATGGGACATCCAAGgtatgcatcc ... acccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC


Block sizes: 37 (upstream exon), 38 (downstream exon)
Score: 10

CTGACCTACTACCTGAAGAAGAAGGTGGCGTCGGAGCGCATCGACCTGGACGTCATCCGCGACGTGGACCTCAACAAGCTGGAGCCATGGGACATCCAAGgtatgcatcc ... acccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC
                                        gactgac  putative branch site (score: 10)
                                              cccctgc  CT-rich tract
                   aaactta  TA-rich tract