Sequence
atgc intronic sequence ATGC exonic sequencegtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ13052 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 10
----------------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
| ||| | | | | ||| | || | | | | | | | | | |||| |||||||||||||||||||||||||||| ||||| | || || ||||| || ||||| ||||| ||||| || |||| || | |
tagctaaggcctgaggtgccatcaatgactgataattgttgttttagactcagttctgatgttgtggttatttatttttgcacatg-tcgaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTAGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 10
--------------------------gtaatac-tcta-ggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
||| ||| || | | ||| | ||| | || | ||| | | || | | | | || |||||||||||||||||||||||||||| ||| | | || || ||||| || ||||| ||||| ||||| || |||| || | |
gtggcgacatcaatcaggtgtcacttgtattacgtccatgaatcctaacatgcttatttattttttgcata-tgtctatttatttggtggaaatgttgcagGTACGTATTTGGAGTGACACACATTCCTCGATTGGAAGACTGGCCTGTTATGCCCGTGGAACGCATTGGTTTCATGCTTATG
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
| || | | | ||| | | || | | ||| || | | | | ||| | |||||||| |||||||||||||||||||| ||| | || || || ||||| || ||||||||||||| ||| || || | |||| |
gataatgaaataaaaaaatatttctttattttctatttttgatatgattttgtgaatttagattagggtgatgtctgataatgtt-gctgaatg-atcgcagGTATGTATTTGGAGTGACACACATTCCTCGCCTGGAAGACTGGCCTGTCATGCCAGTGGAGCACATTGGTTTTAGGCTCATG
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S9_129V6.2 (Physcomitrella patens), 3'ss of exon 5
-------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctag------ttct-cgatcgatgc-aacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
| | | | || | | | || || || ||| | || |||| | || || | ||||||| ||||||||||| || ||||||||||| || || |||||||| || ||||| ||||||| ||| ||||||| | |
cctttacttgtaactttacttgtgggtagggagcctatatatgcgtctgtgaaactgccataatatgcttacatcctttctgcaatttatttgagtgcagGTATGTATTTGGAGTCACTCACATACCTAGACTGGAAGATTGGCCAGTTATGCCTGTGGAGCACATTGGATTCAGTTTGGTG
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S363_39V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgca------acgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
| | || ||| || | || | | | | | ||| || | || ||||||| ||||||||||| || ||||||||||| || ||||||||||| || ||||| |||| | || ||
aggctgttaagttggttggccaggagtaaa-tagagctaataaactccgactttagtgaggtgatgttcttactttcgtaataatttcacctggtgtgcagGTATGTATTTGGAGTTACTCACATACCTAGACTGGAGGATTGGCCAGTAATGCCTGTGGCGAATATGTGA------------
upper sequence: EFJ13052 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------gtaatactc-taggatcgatctctccttcctctcttctcgcaaaatctccta---gttctcgat--cgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
||| | | || | | | | | ||| |||| || | || | | | | | |||||| ||||||||||| || ||||| ||||| || || || ||||| || ||||| ||||||| ||| ||||||| | | |
gggattgttagagtttgcgttgtagtcttaatatggtgaggtatctcaatgtttgttcatgcaattgctgtggtatgctcacactttcctcggagtccagGTATGTATTTGGAGTTACTCACATTCCTAGACTTGAAGACTGGCCAGTAATGCCTGTGGAGCACATTGGATTCAGTTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
aaaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatactctaggatcgatctctccttcctctcttctcgcaaaatctcctagttctcgatcgatgcaacgcagGTACGTATTTGGAGTGACACACATACCTAGGCTCGAGGATTGGCCCGTGATGCCAGTGGAGCGCATCGGATTCACACTCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG