Sequence
atgc intronic sequence ATGC exonic sequencegtttttgtcccatcctttcccaaattaacatcttttcatccctcttccattctatataaaacttgatagtgtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA
Basic information
species | Glycine max |
transcript | GLYMA04G12450.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G014994_T03 (Zea mays), 3'ss of exon 5
----gtttttgtcccatcctttcccaaattaacatctt--ttcatccctcttccattct-atataaaacttgatagtgtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA---
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gttagcctcagtatagagatgattgaatgtagcttggtgacttggtttaaaaccattctgatttccaagcttgtcacaaat-tatgcagACATTACATCAAATGTTTATTGTAAATGCTGGACCTGGTTTCAAGCTGATATGGAGCACTGTTA---AGGGACTTCTTGACCCAAAAACGTCATCTAAAATAC
upper sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G452580_T03 (Zea mays), 3'ss of exon 6
gtttttgtcccatcctttcccaaattaacatcttttcatccctcttccattctatataaaacttgatagtgtatatt-tgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA---
|| | | | | ||| | | ||||||| || | ||| | ||| ||||||||||||||||||||| |||||| ||||| || |||| || ||| ||| | ||| | || ||||||| ||||||| | ||||
--gttagccttagtatagagatgattgaatgtagcttggtttgaaaccattctgattaccaag-gatgtcacaaattatgcagACATTACATCAAATGTTTATTGTAAATGCGGGACCTGGTTTCAAGCTGATATGGAGCACTGTTA---AGGGACTTCTTGACCCCAAAACGTCATCTAAGATAC
upper sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 7
gtttttgtcccatcctttcccaaat-taacatctt-ttcatccctcttccattctatataaaacttgatagtgtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA
|| ||| | | | | || | | || || |||| |||| | | | || || | | ||||||||| || || |||||| ||||| |||||||| | || || || ||||||||||||||||| | ||||||||||||||| | || |||||||| ||||
gtacttgactttctcaattttacatctcatatgttcttcacatgcattcccagttgtttgaagtc--atcatattattttgcagACGTTGCACAGAATGTACATTGTAAATGCTGGAACAGGTTTCAAAAAGATGCTTTGGCCTGCTGCTCAGAAGTTTCTTGATGCAAAGACCATTGCAAAGA
upper sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 6
---------------------gtttttgtcccatcctttcccaaattaacatcttttcatccctcttccattctatataaaacttgatagt---gtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA
|| || | | | | | |||| | |||| || | | ||| | | || || | |||| |||||| |||||| ||||| | |||||||||| ||| |||| || |||||||||||||||||||| |||| ||||| |||||| | || || || | ||||
gtgccttctcttttcatgttatttcttttactgttgtatttgtttttaattgttcaccatctctactaaaaataataattattattattgtcacatgcatttacagACACTACATCGAATGTTTGTTGTCAATGCCGGTCCTGGTTTCAAGAAGATGCTTTGGCCTGCTGCACAAAAGTTCCTTGATCCAAAGACAATATCAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatcttttcatccctcttccattctatataaaacttgatagtgtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA
attctatataaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgtcccatcctttcccaaattaacatcttttcatccctcttccattctatataaaacttgatagtgtatatttgcagACATTACATCAAATGTATATTGTCAATGCTGGTTCTGGCTTTAAGAAGATGCTTTGGCCTGCCACACAGAAGTTTCTTGATTCCAAAACCATTGCGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA