Sequence
atgc intronic sequence ATGC exonic sequencegtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G00760.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagc-tcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||||| ||| | || || || || || |||| || ||| || || || || | | ||| || | | || || | | | || | | ||| | ||||| || |||| ||||| || || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || |||||||| |
-----------------------------------------------------gtagtact-gatcgagttcatagcatctaaattca-----agagggacaattttattggtgaaagat-atatattatttgttaac--ttcttcatttttttttcttttttgtttttaaattttaa------agAGATTTGCAGAATAGGAACAGAAGAACAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACGAATAGAGCGACTGC
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G36600.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
|| | || || | | | || | | |||| | || | ||| | | | || | | | | | || | | | | | | | ||| | ||||| || ||| |||||||| || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || ||||| || |
---------------------------------------------------------------------gta-gaactgatcgagttcaattcatagcatctaaattctagaggggcgattttattggtgaaagatatattgttaactttgcattgtttttttcttttcgttttaaattttaaagAGATTTGCAGAATAGGAGCAGAAGAGCAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACAAATAGAGCAACTGC
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G47680.1 (Glycine max), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttat-aagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | | ||| || | || | | || | || | | | || || | || ||| | | || | | ||| ||||| || ||| ||||||| || || ||||||||||| ||||| || || |||||||| ||||| || |||||||| || ||||| || |
------------------------------------------------------------------------------------ttagtttatagaatt-taaaatcaacatgaaataatattatttgtaaacgatatatcattaattttttggcttcctttcttctttttttgaaaatatga-agAGCTTTGCAGAATAGGAGCACAAGAGCAAAATGAATGGTACTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGCACAAATAGAGCAACAGC
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || | || | || | | | | || | | || | | | || || || | ||| | | || |||| ||| ||||| ||||| |||||||||| || ||||||||||| ||||| || ||||||||||| || || || ||||| ||||| ||||| || |
-------------------------------------------------------------------------------------gtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttt---tattcgtt-tgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | || | | | | | | | | | | | | | ||||| | ||| || ||| ||| || | | | | | | |||| | ||| |||| ||| |||| ||||||||||| ||| ||||||||||| || || || ||||||||||| || || || ||||| ||||| ||||| ||||
---------------------------------------------------------------gtttag-caggaaaatcctatcatctctctttagtagtgatatccttgt---tttggtataaattaaggcttacgattgt------------------tgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagc-atgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacg-gttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| ||||| || |||| | | ||| | |||| || | || | || || ||||| | | | | |||| || ||| | | | ||| | | || ||| |||| || || | ||||||||||| |||||||| ||||| ||||| || || |||||||| ||||| || ||||| || || ||||| || |
--------------------------------------------------------gtatgtagctcttattcctacagtccttccctatgcatacaacagaaaa-----tatgta--tatcttg-atgaaatactatgcatcataaaat-ctgacttccatgttcatttttctta-atttgaatagAGTTATGCAAAATAGGCACTGAAGAGCAGAATGAGTGGTATTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGAACTAATAGAGCTACAAA
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaac--ggttataagccgctaactcacttctacatatg--catggtgacgaaa-cagAAAAGTGCAGGATTGGAAGCGA------AGAG---CAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| | | || | |||||| | | | |||| ||| | | || || || || || | | | || || | || | | | ||| | || | | | || || ||| | | | || | | ||||| |||||||||||| ||| |||| || ||||| |||||||||||||||||||| ||||| |||||||| | |||| ||| | ||| |
gtaagaatcgatcagaatcctcggtgtactatg----tatgacaccagactagaaaacacgtcctcacatgcttcgt-tgccccatttca-gtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgt--acttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC-
||| || || | || || |||| | || || | | | | || || ||| | | || || | | || | || | || | | | | ||| | | | | | | | |||||| |||| || ||||||||||||||||||||||| ||||| || || ||| | || | || |||| || |
----------------------------------------------gcatgaacatgctcatttgaaggacatatttgagtttcgaa-tttctcccacatagagtttttgttttgggattggtggatat----cttgatactgatga-----tattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACG-TCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatg-tacacctcaaagcatgtgtggaacaacaagcttct-tgtggagtcat-tatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAG---------AGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| |||| | | | |||| | | || | | | | | | | | ||| | | | | || | | || | | | | | | | | | | | || ||| |||| | | || | | |||| | | ||| | ||| || ||| | |||| |||||| ||||| ||| | | |||| ||| ||||||||||||||||||||||||||||| || || || || | ||| | ||| |
gtaagccaacgaacccacattttgca----ggatttcattaacgttggttgaggttagaa--aactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactc---taagtactgataacac-catctgtacttgc--ggcgac--atcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtg-acgaaacagAAAAGTGCAGGATTGGAAGCGA------AGAGCA---GAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| | || || | | || || ||| | | | ||| || | | | | | |||| || | || |||| | ||||| || | || | | | | | || | | | ||| | | || || || | ||||| ||||||||| || ||| |||||| | || ||||||||||||||||||||||| |||||||| || || || | || ||||| |
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaaca-gtactatccattgaat-tgtg-atcaacataag-ctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGG-ATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
|||| |||| | || || | || | || |||| | ||| | || ||||||| | | | ||| | | | || | | |||| || | |||||| | ||||||||||| ||||| ||||||||||||||||| ||||||| ||| ||||| |
----------------------------------------------------------------gcaagatcatcacactcaagtgccaacctgaagca--------cgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagc-----gtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaag----catgtgtggaacaacaagc--ttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaa-acagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| ||| | |||||| ||| | | || || || | ||||| | |||| || | || || | | | | || ||| | || | || || | | |||||| |||| | ||||| || |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| || | ||||||||||| ||
----------------------------------------------------------------gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgtt-----ctaaatgtctct---tctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || |||| | | ||| | | | | || | || || || | | | | | | | | |||| ||||| | ||| ||| | || || | ||| |||||||| ||||| ||||||||||||||||| || || || ||||||||||||||||| || |
-----------------------------------------------------------------------------------------------------------gtagtctagtc-tcctccatttcgat--atgattgcacaccactgacacctctttcattgttcttcg-attttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaa-acagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
||| || || | || | || | | | || || | ||||| | |||| || | || || | | | | || ||| | || | || || | | |||||| |||| | ||||| || |||||| ||||||||||||||||||||||||| |||||||| ||||| ||||| || | ||||||||||| ||
------------------------------------------------gtaagacggtcatccctcaag---------cttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgtt-----ctaaatgtctct---tctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
| || |||| | | ||| | | | ||| | || || || | | | | | | | | |||| ||||| | ||| ||| | || || | ||| |||||||| ||||| ||||||||||||||||| || || || ||||||||||||||||| || |
-----------------------------------------------------------------------------------------------------------gtagtctagtc-tcctccatttcgac--atgattacacaccactgacacctctttcattgttcttcg-attttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGCMapped 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|149106166|gb|EE291854.2|EE291854EST: TGTGATAAAAGATGTGGATTTGTACAAGATTGAGCCTTGGGATCTGCAAG AAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCC
genomic: TGTGATAAAAGATGTGGATTTGTACAAGATTGAGCCTTGGGATCTGCAAGgtacatcaac ... gacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
aactcac putative branch site (score: 2)
ttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT