Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggcagtggatctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ26567 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
----------------gtaagtggcagtggatctttgggattgatcggtagttctga--tggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
|| ||| || | | || | | | ||||||| | ||| | | | ||||||||||||||||||||||||||| ||||||||| | ||| | | | ||| | | | ||||| ||||||||||||||||| ||| || |
gtaggtgcttcattccgtctccggccaaggcgacggcgatgtagacgacgatggcaaattcattcgatcggttgggtttttg---cagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
-------------gtaagtggcagtggatctttgggattgatcggta-----gttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
|| | | | | | || | || || || | | || | | | | | || |||||| ||||||||||||||||||||| |||||||| | | |||| | | | ||||| | | ||||| ||||||||||||||||| ||||||||
gtaagcactaagcaccagcaacggcaacgccatccgtttcaacgacgacgatgtgcttacgttttggttcgtgtgcgtgtgt--gcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
| | | | | || | | ||| | | ||| | | | || || | |||||| ||||||||||||||||||||||||||||||||| | | ||| | | | ||| | | | |||| ||||||||||||||||| ||||||||
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc-gcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
----------------------------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
| || | || | || | | | | | ||| || | |||||| |||||||||||||||||||||||||||||| || | | ||| | | | ||| | | | ||| ||||||||||||| ||| ||||||||
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtctgttcctctacgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
----------------gtaagtggcagtggatct---ttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
| | | | | || | | | | | | |||||| | || || | |||| ||||||||||||||||||||||||||| ||||||||| | ||| | | ||| | | | ||||| ||||||||||||||||| ||| ||||
gtacatatatatactagcacataatattaatactgaataagtttctgtttctgctcctgatgatat-ataaatctgatgatggca-cagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggttcg---------atctctcggg----ctatggtg-gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
||| | | | | || | | | | | |||| ||| || || | | ||| | || || | |||| ||||||||||||||||||||| ||||||| || |||| | ||| | | | | | ||| || ||||| || | || | |
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaa--agcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------gtaagtggcagtggatctttgggattgatcggta--gttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
||| || ||| | | || | ||| | || ||||||| | || | ||| ||| || ||||| ||||||||||||||||||||||||||||||||| | |||| || | ||| | ||||| |||||||||||||| ||||||||||
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgcc--gtcgccgtggc-atgctg-cagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
upper sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
-------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggtt-------cgatctctcgggctatggtg----gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
|| | ||| ||| | || || | || | || ||||| ||||| |||||||||||||||||||||||||||||| || |||| | ||| | ||| ||||||| |||||||| | ||| || |
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgctgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
ttctgat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggcagtggatctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG