Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA07G38160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 5
-------------------gtgtgcttaaattaccttctt-ttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctccta--tatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
| | || | | | || || || | | ||||||||| | | | | |||| | | | | || ||||| || | | || | ||||||||||||| || || || ||||||||||||||||||||||| || |||
gttagatactttattcttggcctttctacacttcaaaattattgaagcgactggttggactttggtacca-ttgaatacatcatcattctgctcgctgtttatctttttgtttaatcca--tatatgcagCAATTGGGGCTATCTTCTCAGCAACAGATTCTGTTTGCACCTTACAG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
|| || || ||| | | | || | ||| ||| | | | | || |||||| | ||| | |||| ||||||||||||||| || ||||| || ||||||||||| ||||| ||||||
gtaagccatggctatctttctgcatgatcat--gctggcactaatattgacaccatgtgag--catcatttcctcctgttgactgttatgt---tcaat---gtgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 5
gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
|| || || || | || | | || | || | | || | | || | | | | || | | || || |||||||||||| || || || || |||||||||||||||||||| || |||
gt-tggatatatacttgacccttttcattctctgataatctga---ttagaccatggatgccattgtcaatttgctaaaacttgttttttt-accca--tgtttgcagCAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G701776_T01 (Zea mays), 3'ss of exon 1
gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
|| || || || | || | | | || | || | | || | | || | ||| | || | | || || |||||||||||| || || || || |||||||||||||||||||| || |||
gt-tggatatatacttgaccctttccattctctgataatctga---ttagaccatggatgccattgtcaatttgctaatacttgttt--tttaccca--tgtttgcagCAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
|||| | | || || || | || | | | | | | || | | || |||| ||| | |||||| |||||||||||||| || || ||||| ||||||||||| |||||
-----------gtaccctgaaacaaagaaaaccctt---ttcaagttcttattcattaagtc----tcatactgtttaaatctgtactgatgattt-------tgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
upper sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgcttaaatt---accttcttttacagtaatttgttggacttaactccaaacttggaacattcccttctt------ccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
|| ||| | || || || | || | || ||| | ||| | ||| ||| || | | | | || | || | |||| ||||||| |||||||||||||||| ||||||||||| |||||||| ||||||
gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaa-gttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
tacttac putative branch site (score: 1)
tatatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA