Sequence
atgc intronic sequence ATGC exonic sequencegtctacactttcagagattttgtttctcttgttcttaaactttgctcctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ22278 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 2
-------------------gtctacactttcagagattttgt----ttctct--tgttcttaaactttgctcctttctcgttggtttttca------cagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
| || ||| | | | |||| |||| | || || | | | | || |||| | ||||| ||||||||||||||| || || ||||||||||||||||| || |||||||||||||||||||| | ||||| |||||||| || |
tcagttataaattctagacatatatccttctgatacctgcatatcatcctctagtgttttgaacggttttttatgtatgattttttttgtaaattaccagGCAGTGGCTCTTTTCAAGTCATACTTTGGTGGTGCTTTTGATGAAGATGCTATCAGAAATAACTTTGTTTTAATCTATGAGCTTCTTGATG
upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 2
-----------------------gtctac---actttcagagattttgtttctcttgtt---cttaaactttgctcctt--tctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
|||| ||| | | ||||| | | ||| ||| |||| || ||| | | || | | ||||| |||||||| |||||| || |||||||| ||||||||||| ||||||||||| ||||||||||| | || || || ||||| || |
aactttaaaaatgtcctgttgttttctaaataactcgcggtgatttatctcattctgtatcactttgacttaactacttaatattattcgaaactatcagGCGGTGGCTCTCTTCAAGTCCTACTTCGGTGGAGCTTTTGATGAAGACGCTATCAGGAATAACTTTGTTTTGATATATGAACTTCTTGATG
upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------gtctacactttcagagattttgtttctcttgttcttaaactttgctcctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
|| | | || ||||| | | || |||| | | || |||| | |||||| |||||| ||| | ||||| || || ||||| ||||||||||| |||||||| |||||||||||||| || || || || | | || |
gtaaacttgtttttgtgtttcattttaatattccacaattgttttgattcttgttcaaatttcaagagagtcagattg----attctatacacatactgcttttgattcacattttca--gGCTGTAGCTTTGTTCAAATCATACTTTGGTGGAGCTTTTGATGAAGACGCTATTAGAAATAACTTTGTTCTGATTTATGAATTGTTGGATG
upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------gtct----acactt-tcagagattttgt--ttctcttgttct--taaactttgct-----cctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
|| | ||| | ||| ||| || ||||| ||||||| ||| | | | | ||| | || |||||||||||| |||||||| || || || ||||| || || |||||||| ||||||||||| |||||||||||||| || |
gtgtttaattcagttatgttttagggtgcttgttgaggatcttgaagttggcttgtcgaagtaaacttcttctgaagttaatcttggatgatggtgccagACAGTCGCTCTTTTCAAGTCGTATTTCGGAGGGGCGTTCGATGAAGATGCGATCAGAAACAACTTTGTGCTTATCTACGAGCTTCTTGATG
upper sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtctacactttcagagattttgttt--ctcttgttcttaaactttgctcctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
| | |||| | || ||| | || | ||| | | || | | | ||||| || || ||||||||| || || || || || || |||||||| || ||||| ||||| ||||||||||||||||||||||| || |
gaattaaactgaattatttttgagggtggattttgggaaccagaaaattgatttaaatgcagtgaaagtagttttgaagataattgtatgatggtaccagGCAGTCGCACTTTTCAAGTCGTACTTTGGAGGGGCGTTCGATGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattttgtttctcttgttcttaaactttgctcctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
ctcctttctcgttggt CT-rich tract
ttaaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctacactttcagagattttgtttctcttgttcttaaactttgctcctttctcgttggtttttcacagGCTGTGGCTCTTTTCAAGAGTTATTTCGGTGGTGCTTTTGATGAGGACGCTATCAGAAATAACTTTGTGCTCATCTACGAGCTTCTCGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT