Sequence
atgc intronic sequence ATGC exonic sequence...atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
-----------------------------atcaaacgcga-tcgaattc---atcgcgcgctaactactggctaacaactgctactactactaaagcc--gctagct---ccattccatgcatggaaa-------tcgcg--cgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | | | || ||||| || | |||| | | | | | | | | | | | ||| ||||||| || || || ||| | | | ||||||| || ||||| ||||| || || |||||||||||||||||||||||||||||||||||||||||||||||||||||| | || ||| | || |||||
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactg-gctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | | | | | |||| | |||| | | ||| | ||| | ||| || || | | ||||||| ||||| || || | || || ||||| |||||||| |||||||||||| ||||||||||||| ||||| | ||||| |||||||||||
------------------------gtgatgatttttttgcta--agtagctaagataattaatg--agtag-tgcatgtaat---tgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
-----atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
||||| || || || | || || | || | ||| | | || | | | | || | || |||||||||||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||
gaatattcaaatattgcatcatgggtcatgca-tgac--atgaatcacggc-actaatgc-accattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
atcaaacgcgatcgaatt-catcgcgcgcta-actactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| || ||| |||| | | | || | | | || | | | | | | | || ||| | || | |||||||||||||| || || | ||| ||||| || |||||||||||||||||||| |||||||||||||| || || ||||||||||| |||||||| ||
ttggaatattcaaatattgcatcatgagtcatgctgcatgacatgaatcacggc-atcattttgaggggtttcttttttctttctatctttctt-tttgcagAGAAATGCAAAATAGGAACCACTCCGCAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | | | | | || |||| | | | | | ||| | ||| || || | | ||||||| ||||| || || | || || ||||| |||||||| |||||||||||||||||||||||||| ||||| | ||||||||||||||||
------------------------gtgatgattttttttgctcagtagctaagataattgatg--agtag-tgcatgtaattaattaa---tttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| |||| | | | | | || | | ||| |||| ||| | || | || | |||| ||| | | |||||| |||| | ||||| || || || |||||||||||||||||||||||||||||||||||||| || || ||||| | || ||||| || || |
gttaaaccc--taaatatgaaaaaaaactctttcatttctacgaact--ctctatttctttgttctttatttttgaaccat-tttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
---atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|| | | | | || | | | | | | | | ||||| | ||| | || | || || | ||||||| || || || || | || || ||||||||||| ||||| |||||||||||||| || || |||||||| ||| | || ||| | ||||| ||
catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgtt---atgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0025g02710.t01 (Vitis vinifera), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | | ||||| ||| | | | | || | |||| | | | || | |||||||||||||| || || || ||| ||||| || |||||||||||||| ||||| || ||||||||||| || ||||| | || || |||||||| ||
----------gtaaagccttctctagattcactaccctgtaatgcttcatgat-ttgctttctttgt--gctcatgtttgctctcgaaattt---tgcagAGAAATGCAAAATAGGATCCACTCCACAGAATGATTGGTACTTCTTCAGTCACAAAGATAAGAAGTACCCCACAGGGACAAGAACAAATCGCGCCACCGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0048g02660.t01 (Vitis vinifera), 3'ss of exon 1
-------atcaaacgcgatcgaattcatcgcgcgctaactactgg--ctaacaactgctacta------ctactaaagccgctagctccattccatgcatggaaatcgcgc--------------gcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
||| | | | | || | || || | ||| | | | | | || || | | | || | || || |||||||| || | || || || || || ||||| ||||||||||||||||||||||||||||| || || ||||| || | || || |||||||| ||
gttgtgcttcatatttagttcatcgcctctcattcttttctcttaattttgcaattcttgttgaatattccatcaagatagcgtgtatcttcccctttgtgatgttcatatcggcttgggtttttgcagAGAAGTGTAGAATAGGATCCACCCCTCAAAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCAACGGGAACCAGGACTAATCGCGCCACTGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------atcaaacgcgatcgaattcatcgcgcgct--aactactggctaacaactg----------ctactac-tactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|| | ||| ||| |||| | | | | | | || | ||| | | ||||| ||| | || | || | ||| || | | |||| | | || | | | || |||||||||||||||||||||||||| ||||| |||||||| |||| | || | |||||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAA--GTGTGCAGGATTGGGGACGACCCA-CCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------atcaaacgcga---tcgaattcatcgcgcgctaa-ctactggctaacaactgctactactactaaagccgctagc-tccattccatgcatggaaatcgcgcgcagAGAAATGCAAGA---TCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC-
|| | || ||||||| || | | | | || | | || | | | | | | | | || | || || || | | | | | | || | | ||||| |||||||||||||||||||||||||| ||||| || || |||| || | || || ||||| ||
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------atcaaacgcgatcgaattcatcgcgcgc---taactactggctaacaactgctactactactaaagccgctagctccattc---catgcatggaaatcgc--gcgcagAGAAATG-CAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|| | || || | | || || | | || | |||| | | | || | |||| | ||| || ||| | | |||| || | | || | | |||| ||||||||||||||||||||||||||||||||| || || || || | ||| | |||||
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------atcaaacgcgatcgaattcatcgc---gcgctaactactgg-ctaacaactgctactactactaaagccgctagctccat--tccat-gcatggaaatcgcgcgcagAGAAATGCAAGA--------------TCGGGTCGGGTCCC--------CAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|||| | | | | | | || ||| ||||| | | ||| | | || | | |||||| | ||| | | || ||| | | | |||||| | | || || || || | ||| | ||||| ||||| | |||||||||||||||||||||||| | ||| |||||||
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG---------
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------------------atcaaac-gcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccatt--ccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGG---------TCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|| || | |||| | | | || | | | | || || | || | ||| | ||| ||| | | | | || |||| |||| ||||||| | | | || | |||||||||||||||||||||||||| |||||||| || || || | || |||||||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataa--gctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
atcaaacgcgatcgaattcat---cgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATC----GGGTCGGGTCC-----CCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
|| ||| | ||| | | || || || | | || | | | || | | | || | | |||||| ||||||||| | | | ||| ||||||| ||||||||||||| ||||| ||||||||||||||||| || || | ||| |||||||
--gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccat-tgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-------------atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccatt-ccatgcatggaa-------atcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | || | ||| ||| | | | | | | || | | || || | |||| ||| | | | | |||| ||| || || || | ||| |||| |||||||||||||||||||| |||||||| |||||||| |||||| | |||||| | ||||| |
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgc-gttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| || | | | | | | ||| || ||| | || || | |||| | | | || | | |||||||| || |||||||| || | | || | ||| |||||||| ||||| ||||||||||||||||| || ||||| || ||||||||| | ||||| ||
----------------gtagtctagtctcctccatttcgatatgattgca--caccactgacacctct---ttcatt--gttcttcgattttg---gcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
--------atcaaacgcgatcgaattcatcgcgcgctaacta---ctggctaacaactgctactac-tactaaa-gccgctagctccatt-ccatgcatggaa-------atcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
||| | | |||| || | || | | | | | | | ||||| | | || || | |||| ||| | | | | |||| ||| || || || | ||| |||| |||||||||||||||||||| |||||||| |||||||| |||||| | |||||| | ||||| |
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctac-tactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
| | | | | | | ||| || ||| | || || | |||| | | | || | | |||||||| || |||||||| || | | || | ||| |||||||| ||||| ||||||||||||||||| || ||||| || ||||||||| | ||||| ||
-------------------gtagtctagtctcctccatttcgacatgattacacaccactgacacctct---ttcatt--gttcttcgattttg---gcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
tactaaa putative branch site (score: 1)
tactaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT