Sequence
atgc intronic sequence ATGC exonic sequence...caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
-caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
|| ||| | ||| |||| | ||| ||| ||| ||| || | ||| | | | |||||||||| |||||| ||||| |||||||| |||||||| |||||||||||||| || || |||||||| |||||||||||||||| ||||||||| || || ||||| ||||||
gtagttaactactc---ctgatgttgatatgtgcgaagcaatttt-----gtccttaacgtggcgcaccttaatatcg--ttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
-caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
|| ||| | | | |||| | ||| ||| ||| ||| || | ||| | | | |||||||||| |||||| ||||| |||||||| |||||||| |||||||||||||| || || |||||||| |||||||||||||||| ||||||||| || || ||||| ||||||
gtagttaactacac---ctgatgttgatatgtgcgaagcaatttt-----gtccttaacgtggcgcaccttaatatcg--ttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
----------------caggtaatttctcttgctgacagcgga---atgcctttctcaaattttgtgt-gtctt-tctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
| || | | | |||| | | ||||| || ||| ||| |||| | ||| | || | | || || || |||| ||||| || || || || || |||||||| |||||||| |||| ||||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttc-cccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
--------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
| | ||| || | |||| | |||| || ||| | | | | | | | || | | | || || || |||| ||||| || || || || ||||||||||| || |||||||||| ||||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
gtaactctttcatgtttttagaactgttttggctggtggacaa-gtgatgcaatttgtaaaggggatat-tgtctgctatcagctaatatttttt---tccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
----------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
|| | || | | | ||| | ||| ||||| | |||| | | | || | || | | || | | | |||||||||| || ||||| || |||||||| || |||||||| || | |||||||||||| || || || || | ||| || | || |||||||| ||||||
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttct--agttttctatttacttttttaattttggcttt-------ttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctca---aaatgca-acacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
| | | | | | | | || | ||||| || | | | | | | |||| | | |||||| | ||| | || ||||| || || ||||||||||||||||| |||||||| || | ||||| ||||| || || ||||| | |||||| |||||||| ||||| ||||||
-------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
||| ||||| || | | || || || || |||||| | | ||| | | | | | | || ||| || ||||||||||||| |||||||| ||||| ||||| || ||||| || | |||||||||||| || || || |||| ||| || | || |||||||| ||||||
---gta-tttcttttaataaaag--aaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattt---tgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT----
upper sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
-------------------------------------------------------caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtct----ttctcaaaatgcaacacacctg---aggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
| | ||| | | | | ||| || || | | ||| | || | || | | ||| | ||| | | | | | || |||||||||||| || ||||| | ||||||||| || || ||||||| ||||| |||||||| ||||| |||| ||| || |||||||| ||||| ||| |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
tttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - tgctgac
- - - - - - - - - - - - -gaatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttacatg