Sequence
atgc intronic sequence ATGC exonic sequencegtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
Basic information
species | Glycine max |
transcript | GLYMA09G35970.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G104730_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------------gtaata--catacagctagcttttcaagac-tatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
| || | ||| ||| ||| | ||||| | | | | | || | || || | || | | | | |||| |||||||| || || || || |||| ||||| ||||||||||||||||| |||||||| |||| || || || || ||||| | || | |
gtttggggccatttacctatgacattcctcttgcaatataatggccatgggccatggctgttcagttagtggttcttggtatatctgctgctatgccatctggagtaacagtgc--tttgagtgctgtactactgtactg--ctacgacagGGAGCGCTCCTCTCACGGCGGTGCAGCTGCTGTGGGTCAACATGATCATGGACACGCTGGGAGCTCTGGCTCTAGCCACGGAGCCTCCCAACGACGACAT
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
||| ||| | | | | | || || |||||| | |||||| ||| || | || | | | | || || |||| || ||||| || |||||||| ||| |||||||||| ||||||||||||||||| || || |||||||| || || ||||||||||| |||| || |
gtacgacagaaaa--accaatcaaacaccatctttctt---------ctagcgtttggtcaaatatag-taacca-tttcttttggtttcttttccagGATCTGCTCCACTCACTGCTGTGCAACTGCTTTGGGTCAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCAACAGAACCTCCCAATGAAGGTTT
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
|| || | | || || || | || | ||| | |||| | |||| | | ||| || ||||||| || || || || || || || ||| |||||||||| ||||||||||||||||| || || |||||||| || || || |||||||| | || || |
---gtaagtaaaatcaaacacatgc-acaattttcaccaatgatttttgaataacagtttcagt---aatgattgtttt--gca-----ccttttcagGATCTGCGCCACTCACCGCAGTGCAACTGCTTTGGGTGAACATGATCATGGACACACTTGGTGCATTGGCTCTAGCGACCGAACCTCCCAACGAAGGTTT
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 5
gtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgact----aatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
| | | | || || | | || | |||| | | ||| |||||||| ||| | || | ||||||| || ||||||||||||||||| || |||| ||||| || |||||||||||||| || || ||||| || |||||||||| |||| |||||| ||
-------gtgcgttcatccattaaatctttttccttacaacttaagatttggcgtctatataataaagatgacttagaaatttctttccaagtaattttcagGATCTGCTCCTCTTACTGCTGTCCAGTTGCTCTGGGTGAATATGATCATGGACACTCTTGGTGCATTAGCCTTGGCTACAGAGGCTCCAACTGATGGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
gactaat putative branch site (score: 2)
tccatttc putative PPT
aaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatacatacagctagcttttcaagactatcttttcaggccatagataaatttttggttcaattcagatgactaatcacagcagaaatccatttcagGCTCAGCTCCTCTTACTGCTGTTCAAATGCTTTGGGTAAACATGATCATGGACACCCTGGGAGCATTGGCACTGGCTACAGAACCTCCTCATGATGGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC