Sequence
atgc intronic sequence ATGC exonic sequencegtactttccgagaagttgtcgatccaaggtttttcggtttttgatcgatggtctttggttttgatcgtccagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ36513 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 4
-----------------gtactttccg---agaagttgtcgatccaaggtttttcggtttttg-atcgatggtctttg-----gttttgatcgtcca----------gGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
| || || | | || ||| || || | | || | | | |||||| || ||||| |||| |||||||||| ||||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| || ||| |||| || | ||||||||||
gtatgccagcatattttatgctctctattcgggatatgaatatcagagtttatgcatttctcacactgctggtctgtgtaacttatttgactttccatatgttcctagGACAATGTGCGGAACCAGCTGATCCAGTTTGAATTGCTGCTAACGACCGCAACATTTGTTGTGGCCATTTTCGGAGTGGTTGCTGGGATATTCGGGATGA
upper sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G170326_T01 (Zea mays), 3'ss of exon 5
----------------------gtactt-tccgagaagt---tgtc-gatccaaggtttttcggtttt--tgatcgatggtctttggttttgatcg--------tccagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
| ||| | | || | | || | | | | ||| | | | || || || | |||| || | | ||||||| ||| ||||||||||||||||||| |||||||| || ||||| || || || || ||||| |||||||| ||| |||| || | || |||||||
gtacgtcgacatattttatactctgcttatttgggatatgcatatcaggtttatgcatttcccatactgctggtctgtgttatttgacttgagttccatatgttcctagGACAACGTGCGGAACCAGCTGATCCAGTTTGAGTTGCTCCTAACGACTGCAACATTTGTTGTGGCCATTTTTGGAGTGGTTGCTGGGATATTTGGGATGA
upper sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G064467_T01 (Zea mays), 3'ss of exon 4
--------gtactt-tccgagaagttgt----cgatccaaggtttttcggtttttgatc--------------gatggtctttggttttgatcgtc-cagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
|| || | || || |||| | || | || || | |||| || | | || || ||||| || || |||||||||||||||| |||||| |||| || || ||||| |||||||||||||| || || || ||| | |||| |||||||| ||||
tctctggcctatttgtgtgacaacttgtgcccctgccctgccccccccagtcgtttgtaacagaaaaaacaaagatgctcacagatgctggctgttgcagGATAACGTCCGGAACCAGCTGATCCAATTCGAGCTGCTCCTGACCACCGCCACGTTCGTGGTGGCCATCTTCGGGGTGGTCTCGGGGGTTTTCGGCATGA
upper sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 6
----------------gtactttccg-agaagttgtcgatccaaggtttttcggtttttgatcgatggtctttgg-ttttgatcgtc--cagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
| |||| || | | | ||||| | | || ||| | | || | || ||||| |||||| |||| ||||||||||||||||||||||| || ||||| || ||||| || || || || ||||| || |||| || | || |||||||
gtaatacctcaaaattccatcttccacagctgatattaatccagattgagaatgcacaagagtcatgctgaaaacctcttcaatatctgcagGATAATGTGCGGAATCAGCTGATCCAGTTCGAGTTGCTTCTGACGACTGCAACGTTTGTTGTAGCCATATTTGGGGTCGTTGCTGGGATCTTTGGGATGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|169030774|gb|FE436794.1|FE436794EST: CTCAAGGAGTACATTGACGACACCGAGGATTTCATCAACATCCAACTG GACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCG
genomic: CTCAAGGAGTACATTGACGACACCGAGGATTTCATCAACATCCAACTGgtactttccg ... gatcgtccagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcgatccaaggtttttcggtttttgatcgatggtctttggttttgatcgtccagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
ttttgat putative branch site (score: 4)
tttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttccgagaagttgtcgatccaaggtttttcggtttttgatcgatggtctttggttttgatcgtccagGACAATGTGAGGAACCAGCTGATCCAGTTCGAGTTGCTGCTCACGACCGCGACGTTCGTGGTGGCGATTTTTGGCGTGATTGCGGGTGTTTTCGGGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG