Sequence
atgc intronic sequence ATGC exonic sequencegtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ31748 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g01430.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------------gtttgaaagccgctgactagatattgac-tgtttttgactatgtttgacttc-catgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
|| | | | | | | || || | | | | || ||| | | ||||||||||| |||||||||||| |||| ||||| ||||||
gtacgtacgtgctacggtgctagtgctaactacatatatatatatcctcttccatatactccatccactgatcgatatatatatatgcgcaattatattcatgcgcgtacgcagCTGGACGAGTGGGTGCTGTGCAGAATCTACAAGAAGAAGGAGGCCAACCAGCAGCTGCAGCACTACATCGACATGATGATGGACGACGACAACGATGACG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g03300.1 (Oryza sativa), 3'ss of exon 2
------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgact---tccatgttttt---tcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| || | || | ||| | || | | ||| || ||| | || || | ||||||||||||||||||||||||| |||| |||| ||||
tgagcttgttttattcttggtatatattttattttttagaaaagggttaaagtttgcacgcttctaattattgtttactgcatttgtgattgtccatcagCTGGACGACTGGGTGCTGTGCAGAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAGGAATCAACCGTCGAACAGC
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os12g03040.1 (Oryza sativa), 3'ss of exon 2
----------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttc--------catgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| ||| | | | ||| || | | ||| || ||| | || || ||||||||||||||||||||||||| |||| |||| ||||
gttgattgagcttgtgttttattctttattttaaaaataaataaagcaagtttgcacacttctaattattgtttactgcatttgtgatattgttcatcagCTGGACGACTGGGTGCTGTGCAGAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAGGGATCAACCGTCGATGAAC
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g03300.2 (Oryza sativa), 3'ss of exon 2
-------gtttgaaagccgctgactagatattgactgtttttgactatgtttgact---tccatgttttt---tcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG------------------------------------------------------------------------------------
||| || | || | ||| | || | | ||| || ||| | || || | ||||||||||||||||||||||||| |||| |||| ||||
atattttattttttagaaaagggttaaagtttgcacgcttctaattattgtttactgcatttgtgattgtccatcagctggacgactgggtgctgtgcagAATCCACAAGAAGAGCAACGACTTCAATTCCTCTGACCAACACGACCAAGAACCCGAGGAATCAACCGTCGAACAGCTTGAAGACATCCATGACAACAAC
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os07g37920.1 (Oryza sativa), 3'ss of exon 2
----------------gtttgaaagccgctgactagatattgactgttt--ttgacta---tgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||||| | | | || | | | || | || ||| | || | | || | | | ||||||||| ||||||||||||||||| || ||||| |||| |
gtacgtacgtatatacgtttgtgcgtgacagtctcgct-tggagtcttggactgattgatctgatcaagttgattagtgtctcagCTGGATGACTGGGTGCTGTGCCGCATATACAAGAAGACGAACAAGGCCGGTGCGGGGCAGAGGAGCATGGAGTGCGAGGACTCCGTGGAGGACGCGGTGG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g21060.1 (Oryza sativa), 3'ss of exon 2
---------------------------------gtttgaaagccgctgactagatat-tgactgtttttgacta--tgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | | | || || | ||| |||| | | | | || ||| | |||||||| ||||||||||||||||| || ||||| ||||
tgaaattaatcccttctatttttgatactcttaatttcttaatcatatagtatatgcatccgtgtgattgatcgatcgatgtgcgtggatttttgtgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAAGAAGAGCAGCCACGCGTCGCCGCTGGCCGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCGTGCG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G430849_T01 (Zea mays), 3'ss of exon 3
-----------------------------gtttgaaagccgctgacta-gatattgactgtttttgactatgtt-----tgacttccatgtttt-ttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
| | | | ||| | |||| | | || | ||| || || |||| | |||||||||||||||||||||||||| || ||||| |||
atagctggctgtacgcgttgacagcgacggccatgacggtgacgacgacgataacgtttccttgtttgcatgcccttgctggtgtcgttgttgcgtgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAAGAAGTCCGGCCACGCGTCGCCGATGGTGCCGCCGCTCGCCGACTACGAGCACCTCGACCGCGACGGAC
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G011598_T01 (Zea mays), 3'ss of exon 2
--------------------------------gtttgaaagc-cgctgactagatattgactgtttttgactatgtttgacttccatgtttt---ttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
|||| | || || | |||||| || | | | | ||| | | |||||||||||||||||||||||||| || ||||| |||
atatatatgcatgatatatcctcttcttcctggtttatttgtgcgatggattattattgatcgtctgcgcgcgtacgcgtgcgtggtgtggtgcgtgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAAGAAGGCCAGCTGCCAGGTGCCGGCGATGGCGGCGGTGCCGCAGCTCTCCGACCACGACCAGGACGAGC
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 2
---------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttga--cttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | || ||| | | | || | | ||| | | || | | ||||||||||||||||||||||||||| | || |||| ||||
gtgagtgagactttctttttctttttcttcttttttttttaattgc--acttgct-tgcacggctccagacctgactgaagcgtttcgcatggtttcagCTGGACGACTGGGTGCTGTGCAGGATCCACAAGAAGAGCAACGATTTCCAGTTGTCGTCGTCGTCGGAGCATGAGCACGAGCAGGAGGAGCCGGCGGCGG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G123667_T01 (Zea mays), 3'ss of exon 3
---------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | | | |||| | | || || ||| || | | || |||||||| ||||||||||||||||| || ||||| ||||||
gtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
--------------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | | | |||| | | || || ||| || | | || |||||||| ||||||||||||||||| || ||||| ||||||
aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G123667_T06 (Zea mays), 3'ss of exon 1
------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | | | |||| | | || || ||| || | | || |||||||| ||||||||||||||||| || ||||| ||||||
gtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 2
--------------------------gtttgaaagccgctgactagatattgactgtttttgactat--gtttgacttccatg--------ttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
|| ||| | || || | || || ||| | || | || ||| ||||| |||||||| |||||||||||||||||||||||||| |||||
ttcgttcttatcttagggatatcggaaattaaaaattgaagattaaaatatgtgtgcacatgattgctgacttaattttgatgatttctgatttttgcagCTGGATGACTGGGTGCTGTGCCGAATTTACAACAAGAAAGGTGCAATTGAAAAGCAACAACTACCACCACCGAGTGGGGTCCGCAAAATTGAATGTTCCG
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 2
---------------------------------gtttgaaagccgctgactagatatt---gactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
||| | | | | | || | | | | |||| ||| ||| | || || | |||||||| |||||||||||||| ||||||||||| |||||
ggaaattattcgttctttcttatctctattgaagttagggatatgagaaattgaaaattaaaaaaatgtttgcacatgattgttgtttctgattatgcagCTGGATGACTGGGTGCTGTGTCGAATTTACAACAAGAAAGGTGCAATTGAGAAGCAGCAACCAGCACCGCCACCACCGAGTGGTGTCCACAAAATTGAAT
upper sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv00s0375g00040.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtttgaaagccgctgac---tagatattgactgtttttgactatg-tttgacttccatgtttttt-cagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------
|| | | | | ||| | | || || | | | | | | || ||| || |||| ||||| |||||||||||||| |||||||| |||||
gtatatatggatatgttaatatgcattagtttgtagtctcttatggtattgaaaaaagctcttaatttgttgtgttggatagCTTGACGATTGGGTGCTGTGCCGGATTTACAAGAAGAACATCTCACAAAGGCCAATGGAGAGGGACAAGGAGGAGTCCATGGAGGCCCTGCTTGCATCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG
cttccatgttttttc CT-rich tract
atgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG