Sequence
atgc intronic sequence ATGC exonic sequencegtgaatcgatttctcacatcttcgtctcatagtttctcttggatcctgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAATTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ36083 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ36083 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gtgaatcgatttctcacatcttcgtctc-atagtttctc-ttggatcctgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAATTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGA--AGAGGTTCT-
| | || | | | | ||| ||| || || ||| ||||| || || || ||||||||||| ||| ||||||| |||||||| || ||||||||||| || || || || |||| ||| | || ||| || |
ctctcttttcgtgcatgagaagtactcggtattattcacaggagctgagagactctagtccgttccatctggataacacttcgttttgcgttgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT
upper sequence: EFJ36083 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------gtgaatcgatttctcacatcttcgtctcatagtttctcttggatcctgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAATTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT---
|| | | | || | || | | | ||| || ||| ||| | | | |||||||||||||||||| |||||||||| || || || | || || || || |||| ||| |||||||||
gtgagtttggacagacctgaatttcaccctcttgcaaagaaatgtaggtaaaatgctatgaaatttag-tgagaatttggtcaacatattgc----agGTTTGCAGAGGTGCGGCAAGAGTTGCAGGTTGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCAT
upper sequence: EFJ36083 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G12260.1 (Glycine max), 3'ss of exon 3
--------------------------------------gtgaatcgatttctcacatcttcgtctcat--agtttctcttggatcctgcgag-
| | |||| |||| | | |||| || | | || | |||| |||| | || || ||||||||||| || ||||| ||||||||||||| || |||||||||||||| | ||| || ||||||
gcatttgcttaccttattgtagttacaaaaaatccttaaacattatattttaaacatgaaaataataatgagttactatcacgtactctttgttttccagGGCTTAGAAGATGTGGAAAGAGTTGCAGACTTAGATGGTCGAATTATCTCCGACCTGATATAAAACGAGGAAAGTTCAGCTTGCAGGAAGAGCAAACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatcgatttctcacatcttcgtctcatagtttctcttggatcctgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAATTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT
ttctcac putative branch site (score: 2)
atagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatcgatttctcacatcttcgtctcatagtttctcttggatcctgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAATTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGAAGAGGTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG