Sequence
atgc intronic sequence ATGC exonic sequencegtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------gtactccctgtgtccattggt-tatagatcactc-tttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | | | | | | | | | ||| || | || | | ||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||
gtatttttgcaatgtgaagattcaagctgaaaattctcatgaatcagtatctttttagatgtgttggatgctcacttacataattattctgt-gcagAGGTGCAAGCATTTTGAAATTGGTGGAGACAAGAAGGGCAAGGGAACGTCTCTTTTCTAAACTACCTACTGGATACTGAAGTTGTGGGTCTACTGTGCTT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g33921.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------gtactccctgtgtccattggt-tatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | | | | | | | | | || | | | | |||||||||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||
gtattatttcattgtcaagactcaagctgaaaattgtcatgaatcaatcagtatctttttagatgtgttgggtgctatcttacattattattctttacagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAAACTACCTACTGGATACTGAAGTTGTGGGTCTATTGTGCTT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g33979.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------gtactccctgtgtccattggt-tatagatcactc-tttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
| || | | | | | | | | | ||| |||| || | | | | ||||||||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||
gtattatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctggatgtgttggatgctcacttgcataattgttctct-gcagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtactccctgtgtccattggt-tatagatcactc-tttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
| || | | | | | | | | | ||| || | || | | ||| |||||||||||||||||| | ||||||||||||||||| |||||||| |||||||||||||||
gtatttttgcaatgtgaagattcaagctgaaaattctcatgaatcagtatctttttagatgtgttggatgctcacttacataattattctgt-gcagAGGTGCAAGCATTTTAAAATTGGTGGAGACAAGAAGGGCAAGGGAACGTCTCTTTTCTAA
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------gtactccctgtgtccattggt-tatagatcactc-tttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | | | | | | | | | ||| |||| || | | | | ||||||||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||
gtattatttcattgtcaagactccagagctgaaaattatcatgaatcattattttgctggatgtgttggatgctcacttgcataattgttctct-gcagAGGTGCAAGCATTTCGAGATTGGTGGAGACAAGAAGGGCAAGGGAACATCTCTTTTCTAAATTGCTTGCTACCTACTGGATACTATAGTTGTTGGTCTAC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 3
--------------------------------gtactccctgtgtccat----tggttatagatcactctttgcttactccctgtgtc-acagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
|| | || | || ||| | | | || | | | || | || | ||||||||||||||||||||||| ||||| |||||||| || || || || ||||| |||||
gtataagcgtctcttcccgtcgtttcgtttttgtttttgtcgttttgatcgcgtggctgatgcttgctttcctccttctgtttttgcctgcagAGGTGCAAGCATTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACCTCTCTGTTCTAG
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 3
---------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA-------------------------------------------------------------------------
|| | |||| ||| || | | | || || ||| |||||||||||||| |||||||||||||| |||||||| |||||||| || ||||| |||||
gttagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggctaatggtttgttcctgtctatgt--tgttgtgcagaggtgcaagcactttgagattggtggtgacaagAAGGGCAAGGGAACATCTCTGTTCTAGTTTGCGAATTAGGATTCGCAGCTTTTTATGTTTCAGCAATGTTGGAATCTTTTAGTTTCTCTCTGGATTTTTC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtactccctgtgtccattggttatagatcactctttgcttact--ccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| ||| || | | | | ||||| | |||| | |||||||||||||| |||||||| ||||| |||||||| || || || || ||||| |||||
tacttttgcctcaaacagtaattttgccactgattcccaaacatgctcattgccgttttgaacacgtggttgatgcttgctatgtggttctgttttgcagAGGTGCAAGCACTTTGAGATCGGTGGTGACAAGAAGGGAAAAGGAACATCTCTCTTCTAGATGGAATATTAGAATTTGCAATTTCACACACTCTCTGTAC
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 3
----------------------gtactccctgtgt-ccat-tggt-tatagatcac--tctttgcttactccctgtgtca--cagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | || |||| |||| | | | | | | || || || || ||| |||||||||||||| |||||||||||||| |||||||| |||||||| || || || |||||
gttagtatatggaaagcaatggatgcttttttggttccatgtggtgtgtggctaatggttgttagttcctgtctatgttgtgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCACTCTTCTAGTTTGAGAATTAGGATTTAGAGCTTTATGTTTCAGCAATGT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 3
------------------gtactccctgtgt-ccat-tggt-tatagatcac--tctttgcttactccctgtgtca--cagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | || |||| |||| | | | | | | || || || || ||| |||||||||||||| |||||||||||||| |||||||| |||||||| || || || |||||
gtatatggaaagcaatggatgcttttttggttccatgtggtgtgtggctaatggttgttagttcctgtctatgttgtgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCACTCTTCTAGTTTGAGAATTAGGATTTAGAGCTTTATGTTTCAGCAATGT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G19320.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
|| | |||| ||| || | | | || || ||| |||||||||||||| |||||||||||||| |||||||| |||||||| || ||||| |||||
gttagtatatggtaaacaaaacaatggtttaaagtggttgtttggcatgtgctgtgtggctaatggtttgttcctgtctatgt--tgttgtgcagAGGTGCAAGCACTTTGAGATTGGTGGTGACAAGAAGGGCAAGGGAACATCTCTGTTCTAGTTTGCGAATTAGGATTCGCAGCTTTTTATGTTTCAGCAAT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------gtactccctgtgtccattggttata-gatcactctttgcttactccctgt--gtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
||| | ||| ||||| || | | || | || | | ||| | ||||||||||||||||| ||||| ||||| |||||||| || ||||| || ||||| || |||
gtgcatagaacatagatcagttcattataccggatttgtaacttggtaatttgcttacattgtgttggtttgttgtttatttcagAGGTGCAAGCATTTCGAGATCGGTGGTGACAAGAAGGGAAAGGGAACATCTCTGTTTTAAGTTGGTTTCATCTTATTTTCTGCGATTTTTGTACTTGCTG
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtactccctgtgtccattggttatagatcactct--------ttgcttactccctgtgt--------cacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | | || | | | | ||| || ||||| | ||||| |||||||||||||| |||||||| |||||||||||||| || ||||| || ||||| || |||
gtaatgtctgcgacattctttacctttgttaatcactctttagtctcagttctgtttcttacactttgtgtgtggtttttgcagAGGTGCAAGCACTTTGAGATCGGTGGAGACAAGAAGGGAAAGGGAACATCTCTCTTTTAAGTTGTTGTTTCATCTATCTACTTTTTTTTGTTTTGTTTGG
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| | | |||| | |||| | | || | | || | |||||||||||||||||||||||||| || || ||||| || |||||||| ||||| || ||
gtcagtgtcttgaccatagattactttttccttcttttggtttgctttggcatttggcatagtttttttattattgccattgggttttgcagAGGTGCAAGCATTTTGAGATTGGAGGGGATAAGAAGGGAAAGGGCACTTCTCTATTTTAGATGGATTATTCATGGTCTTTTTTGCTATACTATCTTCCTT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
||| ||| | | | || | ||| | || | |||||||||||||||||||||||||| || |||||||| || ||||| || ||||| || ||
gtcagagtcttaacctcaagctacacttttcttttcctgccttttgtgttacaccccttacttttacacaactgaatttttgttgttgcaattgggttttgcagAGGTGCAAGCATTTTGAGATTGGAGGGGACAAGAAGGGGAAGGGAACTTCTCTCTTTTAGGAGGCAAACTTGGTCATTTTCGTCTTGCTATATTATGTTG
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g02080.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccct---gtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
||| | | | || || | || | || |||| | | | | |||||||||||||| |||||||| ||||| || ||||| || |||||||| ||||| || ||
caaaaatttgtcaaatgtattttttaagttagcaaattttgaaactgtttttaataactgtttccaaatgaacctcagcttctgtcattggattttgcagAGGTGCAAGCACTTTGAGATCGGTGGCGATAAGAAGGGGAAGGGCACTTCTCTATTTTAGATTGCAAAACCAGGCAATTGCAGGGTCCATCTTCCATTTT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S6_198V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------------------------------------gtactccctg----tgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
|| || || || | || | || | ||| | ||| | |||||||| ||||||||||| ||||||||||| || |||||||| || |||||
gtaattcaatctattttcttgctggtagttgattggtttgacaaatattcatgtggaattttgcaacggaattgtcattgtaggtgtaaccattctctcctgtccgtattttctgaaatctttatcatttcgccgatcaaataatcactaggaacgtaccccacttcaaagagtctaacacatgacttggtactctgcagCGATGCAAGCACTTTGAGATTGGAGGAGACAAGAAGGGTAAGGGCACTCAGCTCTTCTAGGCAACTCGATTGGATTACCTCGCTTCTGAACTTTAGAGAG
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S74_73V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
|||| ||| || | || | ||| | | | | ||| | |||||||| || |||||||| ||||||||||| |||||||| || ||||| |||
tggtttcgcgtgcggaagccctcatagtgttttagtctctttgcttacttgaacaatcctcaggcttcaggtgactaacactcaaagtgatattttgcagCGCTGCAAGCACTTCGAGATTGGAGGAGACAAGAAGGGCAAGGGTACCCAACTTTTTTAAACTACATGTCTTAATTGAAATGTTAAAATTGTGGACTGGT
upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S115_63V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtactccctgtgtccattggtta---tagatcactctttgcttactccctgtgtc-acagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA----------------------------------------
| || | || || | | | | | | | || | || ||| | ||||||||||| |||||||| ||||||||||| |||||||| || || |||||
ctccttttctctggggtgttacgtctcatttctctcaagcggtttcacaatgatcacccctcaatttgaagggcctaatacgtagtattaaattctgcagCGATGCAAGCATTTCGAGATTGGAGGAGACAAGAAGGGCAAGGGTACTCAGCTCTTCTAGGCATCACGTCAGGTCCAACTAGAGTCTGGAGTGTTGATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
tgcttac putative branch site (score: 2)
ctctttgcttactccc CT-rich tract
ttatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactccctgtgtccattggttatagatcactctttgcttactccctgtgtcacagAGGTGCAAGCATTTTGAGATTGGTGGAGACAAGAATGGCAAGGGCACGTCTCTTTTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
