Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 2
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatg-catgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | ||| || | | || || || || || | |||||| || || ||| | | |||| ||| || || | | | | || || | | || || || |||| ||||||||||||| || |||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||| || |||||
------------------------------------------------------gtaaaattgaaat---tgagcaatcaatcagtcagctc--atctagctagccggccggagctagcaagcat----gcaacagtgagatttagctgaagtttaaacatggtgattaatatttcatgtggtatatata-cagATCGGTGCAGGATAGGGACGGGGCCTCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCGACGAC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G42050.1 (Glycine max), 3'ss of exon 3
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
| || ||| | ||| |||| || | || || || ||| | | || | | || | |||||| || ||| | | | |||| | ||| ||||| || | |||| |||||| |||||||| ||||||||||| ||||||||||| ||||| || ||||| || || || || || || ||
-----------------------------------------------------------------------------atggaaagaaagacatagacttgttagccttgaaggttataatacttctt------------gagttttttgtagcatgaactagttaacatatgttga---tgctt-cttttcagATAAGTGTAGGATTGGATCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCATAAGGACAAGAAATACCCAACAGGAACCAGAACAAATCGAGCAACTAC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G17140.1 (Glycine max), 3'ss of exon 2
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | || | | ||| || ||| | | | || | || ||| | | ||| || | | |||||| ||| | | | | ||||| | ||| ||||| || | |||| |||||| |||||||| ||||||||||||||||||||||||||||| || ||||| || || ||||| || || ||
----------------------------------------------------------------------------tggaaagaaagacaaaaatatttgttaacta--tgaaggttataatgcttcttgagtttttg---------taacatgaactagttaacatatat-tggtgc-----ttctttgcagATAAGTGTAGGATTGGGTCAGGGCCTCAGAATGAGTGGTATTTCTTCAGCCACAAGGACAAGAAGTACCCAACAGGAACCAGAACAAACCGAGCAACTAC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G79580.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaata-atcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
||| || || || | || || || ||| || | | | ||| || || | | | | || | | || || ||| ||| | ||||| || || | || | ||| ||||||||||| ||||| ||||||||||||||||| || ||||| || || | |||||||| || || |
---------------------------------------------------------------------------------------------tgtgtgtttaaatatatatatatatatacttaagactataattaacaattgtattttttcaattatatttataacaaattttgttgttgtgtgtatg-tagAGAAATGCAGAATCGGGTCGGGTCCTCAAAACGAGTGGTATTTCTTTAGCCACAAGGACAAGAAATATCCGACTGGGACCCGAACGAACCGGGCGACAGC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0085g01210.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaa-ttaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
| | || | | | ||| ||| || || || || ||||| | | || ||| ||| || | | |||| | ||||| |||| | ||| | || || | || ||||||||||||||| ||||||||||||||||| ||||| ||||| || ||||| | || ||||| || || |
--------------------------------------------------------------------------------actaatcagtcc--gcaatacccaaaagcaagattaaagttgatattattgcagtac-----ggtatt------gggaaatttttcatgtttttggatttggttggcatg-cagATAAATGCCGAATTGGATCAGGCTCTCAGAACGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATACCCAACTGGAACTCGAACAAACCGAGCAACCAT
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacag-ctagcaaacatatacttgt-tatatatatacc----tgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
||||| | || | ||| | | ||| || | ||| |||| ||||| | || | | | || | ||| || ||| | | || | | || | || | || |||| | || |||||| | | || ||| | | | | || | | | | |||| ||||| |||||||||||||||||||| ||||| |||||||| |||| | | |||||||
gtaagaatcgatcagaatcctcggtgt-actatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccg-atgtggtcatcagAAGTGTG-CAGGATTGGGGACGACCCAC-CAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgca-gcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactc-acacaaataatcttttatatatgtggaacatgcatgcatg-gcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCG-ACGGGAACAAGGACGAACCGCGCCACGAC-
|| | || | | | | || ||| ||| | | | || || ||| ||| || | |||| || | || || || || || | ||||| || | | |||| | | | | | | ||||| | |||| || ||||||||||||||||||||||| ||||| || || ||||||| | | || || ||||| |
---------------------------------------------------------------gcatgaacatgctcatttgaaggacatatttga-gtttcgaatttctcccacatagagtttttgttttgggattggtg-gatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACG-TCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACC-GTGCAAATCGAGCCACCGCC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
-----gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| || |||| | || ||||| || | ||| |||| ||| | | || | | | | ||||| || | || || || | || | | | | || | | |||||| | || || | | || | |||| |||| | | | ||| | |||||| ||| ||||||||||||||||||||||||||||| || || || |||| | | |||||
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatata-tatatatatatatatatatgagaatactctaagt---actgataacac-catctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCAC----------CCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagtaa-aatacatgt----atgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgca-tgcatggcagAAAGGTGCAGGATAGGC--ACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
||| | || ||| ||| | | | | |||||| || | | | || ||| | ||| ||| | | | ||| | | || | | | | ||| | | | | || | | | ||| ||| || ||| || | | | | |||||| || | || | |||| | | | | || | ||| | ||||| ||||| | |||||||||||||||||||||||| | | | |||||
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtca---atagatttg--------ggacccggaaca---tagccttaaga--actggattga-aaaccacaccacctgatgtgatatttgactccatacttcat-cacctaaaattcgg-gtgt-taaatcatgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG---------
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagta--aaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcga-gctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatctttta-tatatgtggaacatgcatgcatgg--cagAAAGGTGCAGGATAGG--------CACCGG-GCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
||||| | | | || | ||| | | | |||| ||| | || | | | | | ||| | | | | | ||| | ||| | | | || | || | || | | ||| | |||| | |||| || | ||| || | |||| | ||||| ||||||||| || |||| | |||||| | || ||||||||||||||||||||||| |||||||| || || |||| | | |||||
gtaagcatcggaatcctgaaggta-gtatggtgcagtgttcaacctcctcatcta-gtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctatt-gatagcatg---aaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaattttt-ttgcaaatcaaagaga--taactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCA--CCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| || | ||| | | | | || | | | || | ||| || ||| || || || ||| | | | | | | | ||||| || | | | || ||| | | |||||| | ||||||||||| ||||| ||||||||||||||||| || || | | | |||||
--------------------------------------------------------------------------------gcaagatc-atcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCA--------AGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | | | | | |||| ||| || | | | | | | || | || || || | || | || || || ||| | | ||||| ||||| | || ||| ||| | | ||| ||||||||||||||||||||||||| |||||||| |||||||| || || ||||| ||| | |||||
--------------------------------------------------------------gtaagacggtcatccct--caagct---tctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctca------ctgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | | | | | || || | ||| | ||| | || || || ||| | | ||||||| | ||| | ||| || | | | || | ||| |||||||| ||||| ||||||||||||||||| || |||||||| | || ||| | ||||| |
------------------------------------------------------------------------------------------------------------------gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcat-tgt----tcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaatt--aatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | | | | | |||| ||| || | | | | | | | || | | ||||| || || | || | || || || ||| | | ||||| ||||| | || ||| ||| | | ||| ||||||||||||||||||||||||| |||||||| |||||||| || || ||||| ||| | |||||
--------------------------------------------------------------gtaagacggtcatccct--caagct---tctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgt-tctaaatgtctcttctctca------ctgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
|| | | | | | || || | ||| || ||| | || || || ||| | | ||||||| | ||| | ||| || | | | || | ||| |||||||| ||||| ||||||||||||||||| || |||||||| | || ||| | ||||| |
------------------------------------------------------------------------------------------------------------------gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcat-tgt----tcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGCMapped 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|211258975|gb|FL160752.1|FL160752EST: TGTCATAAGGGAGATTGATCTCAACCAGCTTGAGCCATGGGATCTCAAAG AAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCC
genomic: TGTCATAAGGGAGATTGATCTCAACCAGCTTGAGCCATGGGATCTCAAAGgtaagtaaaa ... tgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCC
EST:
gi|93015148|gb|EB640668.1|EB640668EST: TGTCATAAGGGAGATTGATCTCAACCAGCTTGAGCCATGGGATCTCAAAG AAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCC
genomic: TGTCATAAGGGAGATTGATCTCAACCAGCTTGAGCCATGGGATCTCAAAGgtaagtaaaa ... tgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
aactcac putative branch site (score: 2)
acacaaataatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaatttttttgcaaatcaaagagataactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCACCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT