Sequence
atgc intronic sequence ATGC exonic sequence...ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttgagatattgacacataaaatttcttgtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
Basic information
species | Glycine max |
transcript | GLYMA01G01270.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttgagatattgacacataaaatttctt---gtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| | || | | || | | |||| | | | | | | | || | |||| || |||||| || ||||||||||||||||| || ||||||||||| ||||| ||| ||||||| ||||| || |||||||| ||||||||||| || ||||| || |
---------------------------------gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G060611_T03 (Zea mays), 3'ss of exon 17
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaat--gttgagatattgacacataaaatttct----tgtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| | | ||||| ||| | | | ||| | |||||| || | | || |||| ||||| |||||||||||||| ||||| |||||||| ||||| ||| ||||||| ||||| || ||||| |||||||| ||||| ||||| || || |
---------------------------------gtatgctcaccccttggtttctcttgattgtggactgacttttatacttacacattaaggtgttgcactgcagGTTGCTTCCTGGTGGGACTATGGTTACCAAACAACTGCAATGGCCAACAGAACTGTGATTGTAGACAATAACACCTGGAACAACACTCATATAGCAACAG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 17
-------------------------ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttgagat--attgacacataaaatttcttg-tagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| || || | || | | | | | || | |||| | || | || | |||| | ||| || | | || ||||| |||||||| || |||||||||||||| || ||||| || || |||||||| ||||||| |||||||| || || || |||||||| || || ||||| ||||
gtaagttttttcaacaaaaacaagtcagtttttagttcctgttaagcatcatcctttggtagaggtataagctgtctttaatatatgaagttgcctgagtttgatttgcaaaaataaaatcttggtagGTGGCATCATGGTGGGACTATGGTTATCAGACGACAGCTATGGCTAATAGAACTGTGATTGTTGACAACAACACATGGAATAATACTCACATTGCAACTG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 17
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttga-gatattgacacata----aaatttcttgtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| || |||| | || | | | ||| | | |||| | ||| | | || | || ||| | || ||| |||||| |||| || ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| ||||| || |||||||||||||||||||| |||||||| ||||
---tagcaaatcatttctgatagagtttctagctagctaatgcagtatccttaa--cctattgaaggtattaaagaaattagttcttattggaaacttcttgcagGTTGCATCTTGGTGGGACTATGGTTACCAAACTACTGCTATGGCTAACCGGACTGTTATTGTGGACAATAATACCTGGAATAACACTCATATTGCAACTG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: EDP02186 (Chlamydomonas reinhardtii), 3'ss of exon 7
--------------------------------------------ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataa----atgttgagatattgaca--cataaaatttctt----------gtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| || | | || || ||| | | ||| | ||||| || | | | || | | | | | | | | || | || | ||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |||||||| || || || |||||||| | | | || || || || |
gtgggcgggcggaggcagggcgggtaaagggaaagcagccacagcagggggggagggctgtcctgacaccacccagtgcaaaaagcactgctgtcataacccagtcacaagaacacgcaaaaacacaaagtgtcgtgaactcgctcacgtgcgcacgcagGTGGCCAGCTGGTGGGACTACGGCTACCAGACGACCGCCATGGCCAACCGCACCGTCATTGTGGACAACAACACCTGGAACACCTCGCACATCGCCACCG
upper sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S404_37V6.1 (Physcomitrella patens), 3'ss of exon 17
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttga-gatattgacacataaaatttcttgt-agGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
| | | || || | | || | | | | | | | | || || || | | | | || || | | | | ||||||| || |||||||| ||||| || || |||||||| ||||| ||| ||||||| ||||| || || || || ||||||||||| || || ||||| |
--tcgcatgtttgggttgatcaaccgtcaggtcggaattaggcctttcgttctggactcaggattgttttcattgctcttaacgcgtgtttgtgttgaccagGTGGCGTCCTGGTGGGATTATGGATATCAAACAACTGCAATGGCGAACAGAACTGTGATTGTGGACAACAACACGTGGAATAACACGCACATAGCTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctggttaaaacacattataaatgttgagatattgacacataaaatttcttgtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
tattgac putative branch site (score: 2)
tttcttgt putative PPT
ttaaaacacattataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttgagatattgacacataaaatttcttgtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG
- - - - - - - - - -ttacccc
- - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - tgctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - aacacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaca