Sequence
atgc intronic sequence ATGC exonic sequence...gttgcatgtgttaatgcggatattattgccatgatctatgaattttgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
Basic information
species | Glycine max |
transcript | GLYMA16G04240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S33_110V6.1 (Physcomitrella patens), 3'ss of exon 1
gttgcatgtgttaatgcgga-tattattgccatg-atctatgaattt--tgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG-
| | | | | | || | || ||| ||| || ||| | | | ||| || | | || | || | | ||| |||||| | |||| || ||| | |||||||||||||||||||| |||||||| ||||||||||||||||| ||||| | ||||||||||||| | || |
--cggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttc--tgcagcagAAACGA-TGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGCTGC
upper sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S33_110V6.2 (Physcomitrella patens), 3'ss of exon 1
-gttgcatgtgttaatgcgga-tattattgccatg-atctatgaattt--tgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
| | | | | | | || | || ||| ||| || ||| | | | ||| || | | || | || | | ||| |||||| | |||| || ||| | |||||||||||||||||||| |||||||| ||||||||||||||||| ||||| | ||||||||||||| | ||
tgacggacacgcttgtccagaattttcttgtgatgcattgatggtgcggatactaaactatttactcatcagatatcttcctgtgtattcgtttc--tgcagCAGAAACGA-TGGCTTCCCACGTGGTTGGATACCCCCGTATGGGCCCCAAGAGGGAGCTCAAGTTCGCTCTAGAGTCGATGTGGGATGGCAAGACCCAGGC--
upper sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S27_81V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------gttgcatgt-gttaatgcggatattattgccatgatctatgaattttgttgcatgtgttattcg---ttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
|||||| | || | | |||| | ||| || | | | || | |||| |||| | || || | | | ||| ||||| || ||| | || ||||||||||| ||||| |||||||| |||||||| ||||| | |||||| | ||||
acatggaaatggtagaattgcatcttattcacctgatgattagcgtgtgcgaatattcatacgatctctcaggctaacagaaattgttcactgtctgcagACGTT--CTTAGTTAAATCATAAACCATGGCTTCCCACGTAGTCGGATACCCCCGGATGGGCCCCAAGAGGGAGCTCAAATTCGCCTTGGAGTCTATGTGGG------------------
upper sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S399_19V6.3 (Physcomitrella patens), 3'ss of exon 1
---gttgcatgtgttaatgcggatattattgccatgatctatgaattttgttgcat-gtgttat-tcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAA-ATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
||| ||| | | || | || | | | | | | | ||| || | || || || || ||| || || ||| | |||||| | |||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| | ||||||||||||| |
gtggtttagtgtacgtaactgaatgatgcgttggtgcatctcgttcggtatcgaaccgaggtatatcttcgttggctaatgtgttgcacctctctcacagATTTCAAGAACCATGACTTCTCACGTGGTTGGATATCCCCGCATGGGCCCCAAGAGGGAGCTCAAGTTTGCTCTTGAGTCGATGTGGGATGGCAAGACCC------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
attttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcatgtgttaatgcggatattattgccatgatctatgaattttgttgcatgtgttattcgttgtgaactgatttgggattttgatctgttgcgacagAAAAAAATGGCATCTCACATCGTTGGATACCCCCGTATGGGTCCCAAGAGAGAGCTCAAGTTCGCTCTCGAGTCTTTCTGGGATGGCAAGAGCAGCGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- tgcatgt
- -gcatgtg
- - - - - ttaatgc
- - - - - - - - - - - - - - -catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg