Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|||| | || | || ||| | | | |||| || | | | ||| |||| | | | | |||| | || |||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
-----------------------------------------------------aattatgca--catttgattatt-gtttataggcctgc-gatgtccattccacattcagtatt---tgttaagctgagtgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| ||| | | | | | | || | | | |||| | | | ||| ||||| | || ||| | |||| |||| ||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
------------------------------------------------gcttctgattatgcacatttgattgtgttgtttataggcctgctatgtgctttccaataaccagtat------ttgtt---aaatttgtttcatatttcttatgt---atagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgacc--ctccaaataat--aatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatg----ttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || || || | | | |||| ||| ||| | | || ||||| || | || | | || || || | | | | || | | || || | | ||||||||| || || |||||||||||||||| |||||||||||||| |||||||||||||| ||||||| |||||||||| | |||||||| |||||||| |||||||| ||||| |||
----gttttaaccattggtttgctgaatgtgtcttcagtgttgaaaa-atttggacacatttgcttcaaattatgcacattcgactgttgtttataggcctgcgatgtccattccacattcagtatttgttaagctgactgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| | || | | | || | | | || | | | | || ||| || | | |||||||| ||| | ||||||||||||| ||||| |||||||| |||||||||| ||| ||||||| ||||||||| |||||||||| || || || |||||||||||||| ||||
----------------------------------------------------------------------gtaacct---catcttcttcaactctcatccgtttgattgcaca---atttctgattt--caattatggtttgttt-----gtt-tgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| || || ||||| | | | |||| || || | | || | | ||| | ||||| | |||| ||| |||| || || ||||||||||||||| || || |||||||| |||||||||| || ||||||| ||||||||| | |||||||| || || || |||||||| ||||||||||
---------------------------------------attaggtttgattgaattggttat-----tggttatttggtca--tggttgct-----atgctggaaaatgt---taaaatgcttttttcttttgt------tgttgtgaataataaatagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACGCTGCACAAGGTTACCCAATACAAGAAGGGTAAGGATAGCA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || | ||| || ||| || | | | || | | | | ||| ||| || | | |||| || || | | ||||||||||||| ||||| |||||||| |||||||||| ||| ||||||| ||||||||| |||||||||| || || || |||||||||||||| ||||
--------------------------------------------------------------gtaagctcatcttcaatcttcatccctcaactctcatccgtttgattgaaca---actcttgattt--caattatcgttt--tttgtttgct-tgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || | |||| | | | || |||| | | | | | || || | | | || ||||| | || | | ||||||| | | ||||||||||||| || || |||||||| |||||||||| || ||||||| |||||||||| | |||||||| || || || |||||||| || |||||||
-------------------------------------------agtgaattagatttgaaattgcgga--attggttattaggtcgtgtttggtagtacgctgcaaaaatgtta--aaatgcttttcc------ttttgtttgttg-------tgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| || ||| ||| || || ||||| || | | | || ||| | || || | || ||||||| | || |||| | | ||||||||| |||| || || ||||| || |||||||||||||| |||||||||||||| ||| | ||||||||||| ||||||||||| || || ||||||
----------------------------------gttctgaagggcgtatttagattcacttctatgatcgtaattaattctgt-----------atgctgttgaaactgtatcttgtg-gtagttttaa-------acttggttt-------tctgtagGTGAACATTCCGAAAACTAAGAACACTTACTGCAAGAACAAGGAGTGCAAGAAGCATACCTTGCACAAGGTGACGCAGTATAAGAAAGGTAAAGATAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| ||||| | | || | || | || | | | || || |||| | | ||||| | || | || || | | | | | ||| | ||||||||||||| ||||| |||||||||||||| |||| ||| ||||| | |||||||||| | ||||||||||| || || ||||||||||||||||||
------------------------------------ggtgtaaaaagagcct--gttatacttcggttttttagtcttgttatctggct---------ttcttt--------ttcaatatgttttgttga-atatgaaatatatat----tgtctcacagGTGAACGTTCCAAAGACAAAGAAGACGTACTGTAAGAGCAAGGAGTGTAGGAAGCACACCTTGCACAAGGTGACACAATACAAGAAGGGCAAGGATAGCT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| ||||||| | || | | | | | | || ||| | |||||| | | | ||| | | |||| ||||||| ||||| ||||| |||||||| || || |||| ||| ||||||| ||||||||| | ||||||||||| ||||| |||||||| || ||||||
---------------------------------------------------------atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgt-tttggttaaatgtgga--atatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 3'ss of exon 2
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
|| |||| | | | ||| | ||| | | | | | | ||| | | | || || |||| || ||||| |||||||||||||| |||||||| | |||||| |||| || |||||| | ||||||||||| ||||| ||||| || || ||||||
------------------------------------------------------------aagtaaagaaatattagacattggcattgttagatttttttttgcaattctttttcgtaattactttgtttgaatatgaatcattctctggctttggcagGTAAATGTTCCAAAGACCAAGAAGACTTACTGCAAAAGCAAAGAATGCAGAAAACACACCTTGCACAAGGTGACACAGTACAAGAAAGGAAAAGATAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S6_198V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
||| | | | | | | || | ||| ||| ||| || | | || | | ||||||| || ||||||| ||||||||||| |||||| | | |||| || | ||||||||||| ||| | ||||||||||| ||||| |||||||| ||||| |||
------------------------------------------------------gttggttaatggtgcgagatcatgtggatgcgtttagtgtggaggatttgaagaacgat------tgctctattggttttttacttttgtttatggcgtggaccagGTGAATGTTCCTAAGACGAAGAAGTCCTTCTGCCCTGGAAAGGCATGCAAGAAGCATACCCTTCACAAGGTGACGCAGTACAAGAAGGGGAAGGACAGCT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S115_63V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | || | || |||||| || || || || | | | || || ||| | | | | || |||||| | | ||||||||||||||| ||||| |||||| | | ||| | || | ||||||||||||||| | ||||||||||||||||| |||||||| ||||| |||
----------------------------------------------gaatggcggatg----cgtgagccctagtttatct---tgtct---gagtgattgtgcatgttgaatttgaggtttgg----ggctcgtaacttttgttgatggtatggaatagGTGAACGTTCCGAAGACGAAGAAGTCCTTCTGTCCGGGGAAGGCATGCAAGAAGCACACCCTTCACAAGGTGACTCAGTACAAGAAGGGGAAGGACAGCT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagact---cttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | || || |||| || ||| | | |||| ||| | | || || || | | | | | ||| || ||| | |||||||||||||| || ||||||||| | | ||| || | |||||||||||||||| |||||||||| || ||||| |||||||| ||||||||
----------------------------------------------------tagtaga---tctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtg--actctgatg---gaggcttg---catgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S2_415V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaatt--gaccctccaaataataatttat---------------ccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttata-tagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| ||| | || || | | | || | ||| ||||| || | || || | | | |||| ||| || | || | | |||| || | || | | |||| | || | | | | |||| | | |||||||||||||| || || |||||| | | ||| || |||||||||||||||| |||||||||| |||||||| |||||||| ||||||||
gttagcattccatccattccttctgctccggactcagtgcatttgttagttaggattatttcaaaggtgttacatcttcgatgctgctccttgtgatttggatgggacatgcaatgtcagctgtgtgaatagttgtttttggcaattgttaggttttactgttg-atgatcctcactgaggattgcatgatttgctagGTGAACGTTCCGAAAACGAAGAAGTCCTTCTGTCCTGGGAAGTCGTGCAAGAAGCACACCCTCCACAAGGTCACTCAGTACAAGAAGGGAAAGGATAGTC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ05955 (Selaginella moellendorffii), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttt--taacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | | || | | | | | || | | | | | ||| | |||||||||| || ||||| |||||| | | |||| | || | ||| ||||||||| |||||||||| || ||||| |||||||||||||| |||
-------------------------------------------------------------------------------------------------------gtatgttcttgcgaggcgctcgctgctcagatcttagatctctccccaatgccg-acagGTGAACGTCCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 1
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttt--taacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
| | | | || | | | | | || | | | | | ||| | |||||||||| || ||||| |||||| | | |||| | || | ||| ||||||||| |||||||||| || ||||| |||||||||||||| |||
-------------------------------------------------------------------------------------------------------gtatgttcttgcgaggcgctcgctgctcagatcttagatctctccccaatgccg-acagGTGAACGTGCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
ttttaac putative branch site (score: 2)
aaatgttgttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG