Sequence
atgc intronic sequence ATGC exonic sequencegtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ08416 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G147332_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------gtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
| || | || || |||| | | | | | |||||||| || |||||||||||||||||| | || ||||| || || |||||||| || || |||||||||||||| || || || || || |||||||
gtttggcttagaaaaaaccgacacaatatatatctatgatcagagatagtaactaatagatgattgatctatcaatttaattgattggaaat-atgtt---cagGTGACAACTTCAATTTACAATCTCATATTGGGCAAGCTATATTGCGATCACTATGGTACTATGCGCATTCAAGGTAATCGTGAGTATTCATGTAAGCTTA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G157172_T01 (Zea mays), 3'ss of exon 7
-----------------------------------------------------gtagttcaaacggcatttggattggtctaacaccgtacttga--cagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
| || || ||||| ||| || || | |||||||| || |||||||||||||||||| | || ||||| || || |||||||| || || |||||||| ||||| || | || || || |||||||
ttaaatttataatgtttgtcttaggaaaaacctagttaatatatttatgatcagaggtagtgactaatagatgattgacctatcaatttaatatgttcagGTGACAACTTCAATTTACAATCTCATATTGGGCAAGCTATATTGCGATCACTATGGTACTATGCGCATACAAGGTAATTGTGAATATTCATGTAAGCTTA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 7
-----------------------gtagttcaaacggcatttggattggtctaacaccgtacttg-----acagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
|| | | || || | | | | | | ||||| ||||| || |||||||| |||||||||||| | |||||||| || ||||||||||| || |||||||| || || ||||||| || || || || || |
gtaattattatctgcttcaactgctacaatatcctgctttggttctaatttctaaatggacttgttctttcagGTTACTACATCAATATACAATCTCATATTGGGAAAGCTATATTGTGATCACTATGGTACAATGCGTATACAGGGAAACCAAGAGTACTCGTGTAAACTGA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA04G43220.1 (Glycine max), 3'ss of exon 6
-----------------------gtagttcaaacggcatttggattggtctaacaccgtacttg-----acagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
|| | | || || | | | | | || ||| | ||||| || |||||||| |||||||||||| | |||||||| || ||||||||||| || |||||||| || || ||||||| || || || || || |
gtatatattattctcttcaactgctatgatatcctgctttggttctaatttctaaacggactcgttcttccagGTTACTACATCAATATACAATCTCATATTGGGAAAGCTATATTGTGATCACTATGGTACAATGCGTATACAGGGAAACCAAGAGCACTCGTGTAAACTGA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA14G33410.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------gtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
|| | | | | | | || | | | | ||| ||||| || |||||||| |||||||||||| | |||||||| || |||||||| || || |||||||| || || ||||| | ||| || || || || |
gtatatttaactgtttccactaccatgtgtccactatccatgaagaaaattgtgtgttgagatttggttctaaactgatatggagcttttcttc-cagGTTACAACATCAATATACAATCTCATATTGGGAAAGCTGTATTGTGATCATTATGGTACAATGCGTATACAGGGAAATCAAGACTACTCATGTAAACTGA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA13G02610.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------gtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
|| | | | | | |||| | | | || ||||| || |||||||| |||||||||||| | || ||||| || |||||||| || || |||||||| || || ||||||| ||| || || || || |
gtatattttaactgcttaccatgtgtccatttgccacaacgaattctgtgtccagatttggttctaaactggtttggagcttttattt-cagGTTACTACATCAATATACAATCTCATATTGGGGAAGCTGTATTGTGATCATTATGGTACAATGCGTATACAGGGAAACCAAGACTACTCTTGTAATCTGA
upper sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 6
-------------------gtagt-tcaaacggcatttggatt--ggtctaacaccgtactt------gacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
||| | | | ||| |||| | ||| | | |||| ||||| || |||||||| |||||||| ||| | |||||| | |||||||||||||| || ||||||||||| || ||||| || || || || ||||| |
gtatggagcaaatgattggaaagtgtttattctcttttagattccaatttaaaattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
gtctaac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttcaaacggcatttggattggtctaacaccgtacttgacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT