Sequence
atgc intronic sequence ATGC exonic sequencegtaggagcgcgctcgtacttctgattgctctctaaattcttgtggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ09601 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ09601 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
----------------------------gtaggagcgcgctcgtacttc---tgattgctctctaaattcttgt---ggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
||| | | | | ||||| || | ||| || ||||||||| |||||||||||||| || ||||| ||| | ||||||||||||||
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG
upper sequence: EFJ09601 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
----------gtaggagcgcgctcgtacttctgattgct----ctctaaattcttgtg----gcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
| | | | | | ||| || |||| || || ||||||||| |||||||||||||| || ||||||||| | ||||| ||||||||
gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
upper sequence: EFJ09601 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S9_243V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------------------------gtagga-gcgcgctcgtacttctgattgctctcta-aattcttgtggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
|| | | | ||| | | | | || | | | |||||| || |||||||| || || ||||||||||| |||||||| ||||||||
gtttgaattctgcatttataccatctctacttcagctgtatcgaaaatggcattctcttgacgtgtgccttagtggtggtttttctattttctgcttccttaatcgatcaacttaaataacccgttgcacgaaaattcgggactgaggtcagcttgtatgagcatccttgcagCTGGCGCAAGGTGGGACAGCTGTGGGAACTGGTCTCAACACGAAGAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaggagcgcgctcgtacttctgattgctctctaaattcttgtggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
ctctaaa putative branch site (score: 3)
ttcttgt CT-rich tract
taaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggagcgcgctcgtacttctgattgctctctaaattcttgtggcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA