Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgatcgacaacttttgatcgatatatggaggaaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ21317 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g07940.1 (Oryza sativa), 3'ss of exon 2
----gt-acgtgatcgacaacttttgatcgatatatggaggaaccatagcta---gactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
|| ||| || | | | || | | | | || | | | ||| | | | ||| ||| | ||||||||| | |||||||| || |||||||||| | ||| | ||||| ||||||||||||||||| |||||||
gttggtgacgacattgctgcttctccattgcttccggcgtgtctcactgatccatgtctacgtgctcatcatttttttcagACATAGATGGACTGGAAGATACGAGGCTCACTTGTGGGACAACACTTGCAGGAAGGAAGGCCAGACCAGGAAAGGAAGGCAAG
upper sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G04260.1 (Glycine max), 3'ss of exon 3
-----------------------------------gtacgtgatcgacaacttttgatcgatatatggaggaaccatagctagactaatcacgggttt--gatggagC-AGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
| | || | | |||| | | | | || | | || || || | ||| | |||||| | |||||||| | || ||||| ||| |||||||||||||||| ||||||| || || || |||||||| |||||||
gtaggagtaatagattttaatgttttttttaattgttgcatggtttagtgcttt-gtttattttgatgaattttgctcttttttcttttcgtggttcctggattttgttagGCATAGATGGACTGGGAGATATGAGGCCCATTTGTGGGACAATAGTTGCAGAAAGGAAGGGCAAACAAGGAAAGGAAGGCAAG
upper sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------gtacgtgatcgacaacttttgatcgatatatggagg-----aaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
| | |||| | |||| | || | || | | | || | ||||||| | |||||||| ||||||||||| ||||||||||||||||||||||||| |||| ||||||| || || || | ||||| | ||||
gggtgtagagctgaatttaggcttggcgaaggtcga-agtggttgagggtcatgtcctggtctgaggatgttggggggtgtattgtgtgtttgattt-gtagGCATCGTTGGACTGGACGGTACGAGGCACATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG
upper sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------gtacgtgatcgacaacttttgatcgatatatggagg---aaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
| | |||| | | |||| | |||| || | || | | | || | | |||||||| ||||||||||| |||||||| |||||||||||||||| |||| ||||||| || || || | ||||| | ||||
ggcgcagagagctaaattttagcctggcgaaggtcga-agttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgatcgatatatggaggaaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
atatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgatcgacaacttttgatcgatatatggaggaaccatagctagactaatcacgggtttgatggagCAGGCATCGCTGGACTGGACGTTACGAGGCACATCTGTGGGACAATAGTTGTCGAAAGGAGGGCCAGACCAGGAAAGGGAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG