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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT

Basic information

species Arabidopsis thaliana
transcript AT2G41560.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 3'ss of exon 5
------gtacgacagaaaaaccaatcaaacaccat---ctttcttctagcgtttggtca--------aatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
      | |  |    |  |   |||  | |||||    || | |  || | ||   ||        || | |||| | | |  || |   |||  |  ||||    ||||| |||||||||||||| ||  | |||||||| ||||||||||| ||||| || || || || ||||||||||| ||||| ||||| |   |
gtgagggcaacattatagtattcatctgataccatgtatttccattaagtggttccccatgatctccaacacagta-ctaatgtttctctcttccgtcacagGGAGCGCTCCTCTCACTGCTGTGCAGCTATTGTGGGTCAATATGATCATGGATACACTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 5
------gtacgacagaaaaaccaatcaaacaccat---ctttcttctagcgtttggtca--------aatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
      | |  |    |  |   |||  |  | ||    || | |  || | ||   ||        || | |||| | | |  |||    |||  |  ||||    ||||| |||||||||||||| ||| | ||||| || ||||||||||| ||| | || || || || ||||||||||| ||||| ||||| |   |
gtgagggcaacattatagtattcatctgatgctatgtatttccattaagtggttctccatgatctccaagacagta-ctaatgttttgctcttccgtcacagGGAGCGCTCCTCTCACTGCTGTGCAGCTGTTGTGGGTTAATATGATCATGGATACATTGGGAGCTTTAGCACTAGCAACAGAGCCTCCAAATGATGAAAT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
---------------------------------------------------gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccattt----------cttttg-gtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
                                                     | | | |   |   | |    |    | | ||| ||    |    ||     ||  |    |||          ||  ||   | ||    ||||    ||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || || ||  |||||||||| || || |||||||| || |   |
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgctttgagtgctgtactactgtactgctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G31770.1 (Glycine max), 3'ss of exon 3
----gtacgacagaaaaaccaatcaaacaccatctt-tcttctagcgtttggtcaaatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
    ||  |  |  | ||    |    |    | |  |||  |  | ||   ||||  |   |      |  | ||      | || ||||||||||||||||||| ||||| ||  |||||||||||||| ||||||||||||| ||||||||||| || || || || |||||||| || || ||  |
gtttgttggttaatagaatttgttttcccttttataatctgttgactttgtttcaagcaacatggttgatagtctt---ccttctttcagGATCTGCTCCACTCACCGCTGTTCAGTTGCTTTGGGTCAACTTGATCATGGACACTCTTGGTGCATTAGCCCTGGCTACTGAACCTCCTAACGATGGACT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G15800.1 (Glycine max), 3'ss of exon 5
-----gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttctt--ttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
      |    || |||||         |||   |  | || | |  | || |  |||  |    | |||   |||  || |||  || ||||||||||||| ||||| ||||| ||  |||||||||||||| |||| |||||||| || |||||||||||| | || || |||||||||||||| ||  |
gtttgttgattcataaaaattttgtttccactg-cagtgttgttgaatctgtttcaatgaacagccgattaagttttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATTATGGACACTCTGGGTGCATTGGCTTTGGCCACTGAACCTCCCAATGATGGACT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G29010.1 (Glycine max), 3'ss of exon 6
----gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggt-caaatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
    ||  |  |  | ||    |    |    | |||  | | |  |||| | |||  |   |      |  | ||      | || ||||||||||||||||||| ||||| ||  |||||||||||||| ||||||||||||| ||||| ||||| || || || || |||||||| || || ||  |
gtttgttggttaatagaatttgttttcccttttattttctgttgaatttgtttcaagcaacatgggtgatagtctt---ccttctttcagGATCTGCTCCACTCACAGCTGTTCAGTTGCTTTGGGTCAACTTGATCATGGACACTCTTGGGGCATTAGCCCTGGCTACTGAACCTCCTAACGATGGACT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G01360.1 (Glycine max), 3'ss of exon 6
gtacgacagaaaa--accaatcaaacaccatctttc----ttctagc-----gtttggtcaaatatag-taaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
|||  ||| | |   | |  |  || || ||||||     |  ||||      ||| ||  ||| ||| | || | |       |  ||  || |||| |||||||| || |||||||| ||| |||||||||| ||||||||||||||||| || || |||||||| || || |||||||||||  |||| ||  |
gtaatacatacagctaactttttaagacgatcttttcaggtcatagctaaatatttagttcaatttagatgactaatcacagcagaatccatttcagGTTCTGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGCGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
gtacgacagaaaa--accaatcaaacaccatctttctt---------ctagcgtttggtcaaatatag-taacca-tttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
|||  ||| | |   | |  |  || || ||||||              |   ||||||  |||  || | || | |  |    |   ||  || |||| || ||||| || |||||||| ||| |||||||||| ||||||||||||||||| || || |||||||| || || |||||||||||  |||| ||  |
gtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G32780.1 (Glycine max), 3'ss of exon 5
gtacgacag--aaaaaccaatcaaacaccat--ctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttctt--ttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
||  |       | || || |      |||   |  | || | |  | || |  |||  |  | | ||||| |||  || |||  || ||||||||||||| ||||| ||||| ||  |||||||||||||| |||| |||||||| || ||||| |||||  | || || |||||||||||||| ||  |
gtttgttgattcataaacattttgtttccactgcagtgttgtcgaatctgtttcaatgaacaaccgatttcattttcttccttattttcagGATCTGCTCCCCTCACAGCTGTTCAGTTGCTTTGGGTCAACCTGATTATGGACACTCTGGGTGCTTTGGCCTTGGCCACTGAACCTCCCAATGATGGACT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g08960.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
                                                   ||||    | | ||     ||| || || |   |  | |   |      ||  ||| | |  |     ||||        | |||||||||| ||  | || ||||| ||  |||||||||||||| |||| |||||||| || |||||||||||  | || ||||||||||| || || |   |
gtgcgttggcccatggagctagtcttttcatttcatgtagtgctcttatttgtacttttgcataatatgccaatcaacaacag-cagcaataatgataataataataatgataaggatctttgaaacaacattcagGATCTGCCCCCTTTACGGCTGTCCAGTTGCTTTGGGTCAACTTGATTATGGACACTCTCGGTGCATTGGCATTGGCGACAGAACCTCCAAACGATGCACT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 5
----gtacgac-agaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaacc-----atttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
    || |  | |  ||| |   |     || |  |    | | |||| |    ||  |   | ||      ||||||||     |  ||| ||||||||||||| || |||||||| ||  |||| ||||| || |||||||||||||| ||||||||||| ||  | || |||||  |||| | ||| ||  |
gtgcgttcatccattaaatctttttccttacaacttaagatttggcgtctatataataaagatgacttagaaatttctttccaagtaattttcagGATCTGCTCCTCTTACTGCTGTCCAGTTGCTCTGGGTGAATATGATCATGGACACTCTTGGTGCATTAGCCTTGGCTACAGAGGCTCCAACTGATGGCCT

upper sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ18007 (Selaginella moellendorffii), 3'ss of exon 3
gtacgacagaaaaaccaatcaaacaccatctttcttctagcgtttggtcaaatatagtaaccatttcttttggtttctttt-ccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
                  | | |  |  |  |  ||      || ||||  |||| || ||  |||||| |  | || ||   ||||  | ||||| |||||||||||||| ||||| ||||| ||  |||||||||||||  | |||||  | ||||| ||||| || || || |  || | | |
-----------------gtaagattctttactctttaagttcttgggtctcatat-gtgactttttcttctcttgtcgttgatcagGGACGGCTCCGCTCACTGCTGTGCAGCTGCTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttctagcgtttggtcaaatatagtaaccatttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
                        tagtaac  putative branch site (score: 1)
                              ccatttcttttggttt  CT-rich tract
                   aaatatagtaa  TA-rich tract