Sequence
atgc intronic sequence ATGC exonic sequence...tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaatgtaaatactaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
Basic information
species | Glycine max |
transcript | GLYMA06G09100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 4
----------------------------------------------tgttgtctagt-actatttaatactttggccatgcacttgttttttttttttttgttaattgcgta-atgtaaatactaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
|| | | |||||| || | || | || | | | | | | | | ||| | | | || | | ||| |||||||||||||||| ||||||||| |||| || || || || ||||| || || || || || ||||||||||| ||||| | || ||| | |
gttggtcacggcctctgaatcactactactatttcgcttgcttgtttgcctctgaatcactattatattccttcctcgcgcggcttaactgaactgctccatcgttcttgcctacgtactctccattccatgggc---acccttgcagCCTGGTCCGGATTCTATTGGAATCATTGCCATCTCGCATGGCTGCCCCGGTGTCGCCGCGCGAGCTTGCGGCCTCGTGGGCATGGAGCCTGCGAAA
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaat-gtaaatactaatttttgttctgaat--gtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
|| || ||| | | | | || |||| | || ||| | ||| || || | | | || ||||||||||||||||||| |||||||||||||||||||| || ||| | ||| | ||||| ||||||||||||||||||||||| || || || |||
-------------------gtaattc--tcataagtctatctcgtcttcttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 4
----------tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaatgtaaatactaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
||| | | | ||| || | || ||| ||| || | | || | || |||||| | || | || | | ||| || |||||||||||||||||||||||||||||||||||||||| |||||| |||||||||| ||||| || ||||||||||| ||||||| || || ||
tgggtgacattgtggctt--tgctacaatatcttctgaccaaa-actagtcctgtgttcctgctcctttttcgtaatctctat-ttgatctgtcccctg------tgcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGAGTGGCAGCACGCGCATGCGGCCTTGTCAGTCTAGAGCCAACAAGA
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S70_192V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------tgttgtctagtactatttaatactttggccatgcacttgttttttttttt--tttgttaattgcgtaatgtaaatactaat-------ttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG----
|| | | ||| || || | || | | ||| | |||||||| || || | | | || | | | || | |||| |||||||||||||| ||||||| || ||||||| || ||||||||| ||| | ||||| || ||||||||||| |||| || || || | |
gtatgtcatctctccgcgatggtgatgagtgattcaccgcatcacctcttaccgtaatctgagtgatttgaagtaattgcaatgctctgaaattgaaatctgaagttctgaaagggcggtttggctgaatttgttaactg-gtgagactattgctgttgcactaatagtaagatgtttatttgcagCCTGGTCCGGATGCCATTGGCATTATTGCTATATCCCACGGTTGCGTTGGTATAGCTGCTCGAGCTTGCGGCCTAGTGGCCCTCGATATTAGTAAGGTAA
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S67_107V6.1 (Physcomitrella patens), 3'ss of exon 7
tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgt-taattgcgtaatg--taaatactaatttttgttctga-atgtttgt--agCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG----
|| | | || | ||||| | | | | || | | || | ||| || | | || |||| | | || | ||||| |||||||||||||| ||||||| || |||||||||| ||||||||| |||| | ||||| || || ||||||||||||| || || || |
------ttatctcaagttctgaatttggtgacgaattgaaattcacagaagtggaatacatacgtcattatttagaacaaattaacggtgagatgtttttgtgcagCCTGGTCCGGATGCCATTGGCATTATTGCTATTTCCCACGGTTGCGTTGGAATAGCTGCTCGAGCGTGCGGCCTTGTGGCCCTCGATGCTGGTAAAGTTA
upper sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S55_99V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaatg------taaatactaatttttgttctgaa--tgtt-tgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG----
| | | |||| ||| | | | | | | | | | || |||| | | | ||| |||| | | ||| || | | |||||||||||||| ||||||| ||| ||||||| || ||||||||| |||| | ||||| || ||||||||||| |||| || || ||| | |
gtatgaaatttcttcgagatggtcttcacttcgcggactgagtatggtgactacttgtggagtgaatcacctcttacacacctatccaatgatgttgtattacccaatgtgatctcaaaaacgtcaattacatgcagcgctattaagctctaactaacgagctggtgttgctctccagCCTGGTCCGGATGCCATTGGCATCATTGCTATATCCCACGGTTGCGTTGGAATAGCTGCTCGAGCTTGCGGCCTAGTGGCCCTCGATGCTAGTAAGGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgttaattgcgtaatgtaaatactaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
tactaat putative branch site (score: 1)
taatgtaaatactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaatgtaaatactaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
tgttgtc
- - - - - - - - - - - ctttggc
- - - - - - - - - - - - - - -catgcac